If you truly feel that way why would you be ashamed to show it?

I wouldn't worry about it too much. They're probably looking more for whether you can write well and less about the paper's topic.

That's the whole point of academia, I'm sure you'll be fine. Where would we be if fundamental views weren't challenged?

If its actually a good criticism, I'm sure the prof would like to hear about it. Remember, it's research, there is always room for criticism.

Your screwed. Sorry.

I can see this being the beginning of a long battle!

Seriously if you wrote an intelligent, well reasoned argument about his research it might prove to be a real asset and something that may let him see you in a very favorable light. It would me.

OP, if he's a good professor, he won't care what your opinion is as long as you can defend it well. After 6 months and 40 pages, your argument seems well prepared! Just make sure you avoid ad hominem attacks and there shouldn't be a problem.

Hopefully he's professional enough to take criticism.

Great minds think alike, but they only become great by debate and discussion. How can he be biased by your POV, that's not fair?