Title says it all, really. The Scoobies were at one time among my favorite group of fictional characters ever. They still are, in many ways, especially in the early seasons: the group of lovable outcasts who banned together to protect each other, do good and, on occasion, save the whole damn world. Buffy gathering a group around her was one of the many factors that made her such an effective hero, and the narrative points out several times that her friends are what make her the most effective Slayer to date.
The idea of the badass, "lone wolf" hero is a very patriarchal idea, typically a male fantasy: we see it in several sources of media, like the various Clint Eastwood Westerns, or comic book characters like Batman and Wolverine*. It's an idea that many are drawn too, myself included, but it's not all there is. Forming a collaborative effort between individuals to give everyone a purpose and to accomplish larger goals is sometimes viewed as a more feminine ideal, and it's no coincidence that we see it present in the narratives of many female heroes: Buffy herself and the Scoobies, Sailor Moon and the Sailor Soldiers, Wonder Woman with both the Amazons and the Holliday Girls, etc.
So on a symbolic level, the Scoobies resonate with several people because they represent a worthwhile ideal. Even all the way to the current comic book continuations, what they represent has never really changed. However, their individual characters have taken one disastrous nosedive after another, and what's worse, they are rarely (if ever) called out on it. And it seems more and more apparent that they never really will be.
All the way back in season two, the black/white morality the Scoobies lived by made sense. They were teenagers, and the series acted as somewhat of a cautionary teen fable, where actions lead to serious consequences and lessons were learned. The Scoobies, despite their realistic individual flaws, were good, innocent kids. So their respective reactions to the crimes perpetrated by Angel/us and Faith are not unexpected. Having one of your best friend's boyfriend turn into a psychotic killer and murder one of your other friends (and countless others) is some seriously heavy shit, guys. Even though ensouled Angel isn't really to blame for what he turned into, I'm not sure if I'd want to be anywhere near him either if I was in their shoes. In fact, Giles is a major class act for tolerating the B/A romance throughout season 3, most likely because he intellectually knows their is a distinction between the man and the demon. Xander comes off much worse, but again, he's a teenager dealing with some seriously heavy trauma; most adults would handle the same way, if not worse.
Faith is a similar deal; a girl your barely friends with killing people and nearly raping/killing one of your friends wouldn't inspire much loyalty. The Scoobies ultimately failed to give Faith the help she needed, but they weren't emotionally equipped to do it at their young ages. Giles is more to blame, being the responsible adult here and playing blatant favorites with Buffy. Still, the Scoobies are adhering to their black/white view, and aren't committing any of the evil deeds their condemning others for, so they are still heroes in my eyes.
Then Anya joined their group, and things started to get weird. Anya, who willingly chose to become a demon (making her far worse than Liam and William), and who likely had a higher body count than the entire Fanged Four combined, was allowed into their social circle, despite being an unrepentant mass murderer. Even the fact that she was a "harmless" human didn't negate her threat level, as her antics in "Dopplegangland" resulted in the death of at least one person. But she was funny, and Xander (inexplicably) liked her, so she was allowed in. The other Scoobies didn't seem to like her, but that seemed more due to her being obnoxious/off putting than being a former demonic killer. I've already covered them keeping Spike alive for increasingly dubious reasons in another post, so let's just say a pattern was forming here and it was starting to get ugly.
But, despite the company they kept, the core Scoobies remained lovable characters. Some of the arrogance that would take over Willow's character later on started to creep in during season 5, but not so much that it overtook her status as a hero. Once season 6 started, however, all bets were off.
Let's start with Willow herself: resurrects Buffy using an extremely dangerous ritual for selfish reasons, manipulates her lover's mind and later the minds of all her friends, spirals into an addiction, tortures and murders a man in cold blood, comes close to turning Dawn back into the Key (which would effectively kill her) and nearly destroys the entire goddamn planet. What does she get as punishment? A bitchin' vacation riding horses on Giles's ranch, apparently.
To be fair, Willow judges herself harshly for her actions, and her appearance in AtS depicts her being friendly to Angel and a lot more civil to Faith than she had been previously. It's possible she feels she can no longer judge them, as her own actions as Dark Willow make her no better than them. But the fact that the narrative, the Scoobies and even most of the fandom gives Willow a free pass is seriously troubling.
Xander's almost as bad. First of all, his dating of Anya and continuing to judge Buffy's taste in men is hypocritical on an astronomical level. Buffy is a saint for not calling him out on his BS until "Selfless," and even then she doesn't really give him the verbal smack down he really has coming to him. But worst of all is "Once More, With Feeling," where it is revealed Xander summoned Sweet (?!), resulting in the deaths of at least one person that we know of. Not only does Xander not show any remorse at all (making him come across as a total sociopath), but the incident is handwaved and never brought up again, making Xander the biggest Karma Houdini in the mythos. The fact that he still acts holier than thou towards Angel is infuriating.
Buffy herself comes across better than the other two members of the Three Musketeers, considering her clinical depression is due to their actions in the first place. Still, her actions in "Gone" are pretty damn bad: I'm talking about her most likely costing that social services woman her job. Yeah, the woman was kind of annoying, but she was doing what she thought was in Dawn's best interest, and let's face it, Buffy and Willow were really shitty guardians anyway. Her arrogance in season 7 is through the roof, and as obnoxious as the Potentials were, I can't really blame them for wanting to kick her out.
When you read the rap sheet, it will come as no surprise that I prefer Angel's crew to the post-season 5 Scoobies any day of the week. This point is driven home in "Damage," where Andrew (ugh) is dispatched by Giles to contact Wolfram and Hart to retrieve Dana. Dana, who was empowered against her will by Buffy and Willow's actions, and who then went on to kill at least two people that we know of. Andrew then informs Angel that nobody in the Scooby camp trusts him because he signed up with Wolfram and Hart: the same organization that Andrew/Giles had no problem using the resources of to help clean up Buffy's own damn mess. I think the scene was meant to make Angel question his actions, but it really only made me think "wow, the Scoobies are total dicks."
Buffy's more idealistic view point on good/evil only contrasts well with Angel's more pragmatic approach when Buffy and her cast live up to those ideals. Instead, they are the biggest hypocrites in the shared universe, something that I don't believe Angel or his crew ever really were. Angel is constantly blaming himself for his crimes, and receives several karmic punishments throughout the series for both his actions as himself and as Angelus. Can you really say the same about any of the BtVS characters?
*Though these two are often a subversion; they harp on about being loners, but they're rarely alone, as the various Robins, Batgirls and fellow X-Men can attest.