I think that part of the reason that a lot of people on the left don't like him, is that he is not as theatrical and bombastic as Hannity, so Colmes comes off weak on TV when they are together.
Another reason is that, I believe, many on the left view him as sort of an "Uncle Tom" one-and-only house Liberal at Fox, both radio and TV.
Some of my Liberal friends (I have all kinds because I am a moderate independent) have made the point to me that if you are going to have only one voice on Fox against loud, bombastic types like Hannity and O'Reilly, then they should have at least picked a pit-bull like James Carville.
Also, something that I noticed myself. I saw an industry publication which had a bunch of Fox full-page ads in a row, each featuring a different personality. The Hannity full-pager showed a soft-focus Hannity staring into the camera in front of a flag with his arms folded, with the tag line something like: "Sean Hannity: America's Concience". The O'Reilly had a flattering, soft-focus shot of him staring into the camera with the tag: "He's always looking out for you".
The Alan Colmes ad showed this extreme, close-up face, sharp focus shot of Colmes with a kind of spaced-out look, his eyes divered off camera. The tag was (I swear!) "Alan Colmes: He May Be A Liberal, But He's Not Crazy!"
Even to me....who is suspicious of all media consipracy theories left or right........this sure looked a little like Fox marketing was screwing with him.