Unlikable Characters

I've been working on my novel and trading reviews via an online writing community and from an offline source as well. Critiquing and being critiqued is one of the most interesting parts of writing but also one of the scariest. A writer puts a lot of herself into her work. It's one thing to point out or to have someone point out a few comma errors or an awkwardly worded sentence, or even a plot loophole. It's another to have someone criticize your basic premise or, horrors or horrors, your characters.

"I think you've got a good story going here, but I'm going nuts because I'm not sure I like your main character." I just received this bit of feedback from someone who had just finished my first few (revised) chapters. I'm certainly not setting out to write my characters as me, and for all that they contain aspects of myself, I think I've been successful at making them unique. I know it's a strange analogy, because I've created these pretend people from scratch and my own imagination. Nothing about them should surprise me. Yet, I honestly can't say that they (or the story) unfolded exactly as I envisioned when I started writing. In some ways, they're like virtual offspring. I cherish them in spite of their flaws. It's hard not to feel defensive when someone says he dislikes one of them, even if the character is question is a bit like a troubled child who hatched out of a cuckoo's egg. He didn't get all that angst from MY side of the family--honest!

Of course, I hope to get more feedback about what it is the reader dislikes about the character. Is it due to something that I can, or should, alter? Does he think the character is vapid and unconvincing, or is the character so believable that his flaws are frustrating in the way a real person's flaws are frustrating? Most importantly, is the 'not liking' the kind that would lead the reader to put the novel down, or the kind that draws the reader in?

Characters don't have to be 'likable' to be compelling. I didn't 'like' Thomas Covenant during most of Donaldson's first Trilogy, but I found the character interesting and relatable at a certain level, and I became invested in his story. In fact, my main character is meant to be a rather disturbed and conflicted person. Early on, he's dealing (or perhaps failing to deal) with the consequences of some rather horrible things that have been done to him and some rather horrible things he's done. In fact, the protagonist doesn't like himself at first.

Not everyone wants to read a story where the plot driving character is deeply flawed (though it certainly leaves room for the character to grow and change throughout). But not everyone wants to read a story where the protagonist is Mr. or Ms. wonderful either. So what I really want to know is whether the character being perceived in the way I intended him or her to be? Is my intended portrayal of the character something that at least some readers will find intriguing enough to get into the story and hopefully start caring about him/her and his situation in spite of his/her flaws?