The whole point of Warren is that we're supposed to hate him, and the fact that you're asking why so many people hate him is a perfect way of showing that Joss and co got the character perfect in every way!
Warren is the epitome of alot of the bad things that man can be in real life. I love that the as a bad guy, he's real and believable, in the sense that you could quite easily meet a Warren while walking down the street. I dated one for a year, and the character of Warren and the way they made him was perfect.
While he hates women, he fears them, and this is where his misogynistic tendencies come from. He has no real love for women, beyond a desire to control, which is what's shown first with April ('I was made to love you') and then subsequently in 'Dead Things', where he enslaves Katrina against her will. He didn't love her, not in the normal sense of the word, but loved the idea of having power over her, having a woman who he could get to do everything he wanted.
He becomes increasingly unstable as the season continues, as his life starts to unravel and people realise what he's really like (i assume that up until Dead Things, Jonathon and Andrew had no idea what Warren was really like, as he probably went to some trouble to come across as something different, or at least make his misogynism 'cool' and probably somewhat harmless).
So Buffy, to him, represents everything he hates in women- she is stronger than him, both physically and mentally, she can't be bullied or intimidated (which is sort what they are trying to do when they test her in 'Life Serial') and to be honest, she's not scared or put off by him and is little group in the least (where she asks if they've banded together to be pains in her ass).
He can't deal with that (I guess alot of men would have a problem with a woman being so much more powerful than they are... even Xander has made reference to it every now and then, and has had slight struggles with it) and so he becomes more unhinged, eventually going to any length to 'cut her down to size' as it were, showing he has the power and he can do what he wants, she can't stop her, and he is basically, better than her; and so shooting her, and accidently killing Tara in the process.
So basically, he's created to be the epitome of a person you could quite easily find in everyday life, and I think alot of people (concious or subconciously) pick up on that, and that's why the hatred for him goes deeper than with alot of the other villans in Buffy... I certainly hate him the most out of all the villans for that reason, anyway.
[sorry that this was such a long post.... i get carried away sometimes!]