*Or not technically "Sebastian Verlac" - he stole the name from Aline's cousin. Oh, yeah, spoilers for the Mortal Instruments ahead...
In the vast majority of YA fiction there's three main guys - bad-ass good guy, not-so-bad-ass good guy and evil guy (usually bad-ass too) - and The Mortal Instruments is no exception. You've got Jace, Simon and "Sebastian". To put this is a context that more people will understand - not that TMI isn't well known - think Harry, Ron and Draco from Harry Potter. So person A (bad-ass good guy) is the main protagonist, the hero, the one who everyone is supposed to fall in love with, but it doesn't always work out that way. The root of why this is lies in the answer to another question. "Why do we read?"
Primarily, we read fiction as an entertaining escape from reality. To run away to a place in which more interesting things happen and anything can happen, all from the comfort of a safe place in which we don't have to worry about getting killed or being in any other tangible danger. And this is why everyone roots for the bad guy really.
We love the IDEA of danger and the temptation to do things you shouldn't. It fascinates us at a base level. It might be completely demented and immoral, but it's still fascinating. For instance, Draco is a completely horrible snob, he bullies - and even curses - other people, just because he can. Is it wrong? Yes. Does he still have one hell of a large fanbase? Of course. The point is, he's thrilling. He does things that most wouldn't ever think of doing and it makes people think "why?" while they wonder what he'll do next. Plus he's hot, that always helps.
Now apply that to Sebastian. He's Clary's brother and comes onto the scene in the third book, masquerading as the cousin of Aline Penhallow. He - knowing exactly who she is - kisses his sister, takes down the city wards preventing the demons from swarming in and murders Max and Hodge, but on the other hand he tries to help Clary, he seems to actually love his father and from the excerpts from CoLS he even kills a demon - technically one of his kind - to save his sister who he hadn't really seemed to care too much about. Is he evil? Most definitely. Is he still just as fascinating? Obviously. Sebastian has a very strange, almost blue-and-orange sense of morality which makes him my favourite character in the series, just because I have no idea what he'll do next.
Disclaimer: No matter how much I love this character, if I ever see meet anyone like Sebastian in real life then I'm turning tail and running as far as I can. Because being that evil and cruel in real life is just not cool. And it's sick.