Yes, on the Bioware forums I've noticed it a lot too. In KoToR, a lot of people hate Carth. In Mass Effect, a lot of people hate Kaiden. In Dragon Age: Origins, a lot of people hate Alistair. In Mass Effect 2, a lot of people hate Jacob.
I'm not going to even guess why people hate them, but I will try to analyze the similarities between them.
They are all the male leads in each of their respective games (introduced the earliest in the game and tend to have the most coversations or interactions). They're all designed to be fairly "normal" personality-wise, at least when compared to the majority of the cast (who tend to exhibit extreme, yet stereotypical, personalities).
I personally found nothing wrong with any of them. Jacob is one of my favorite supporting characters in ME 2, despite the amount of hate that he gets, as well as Alistair from DA:O.
