I think you've described the "problem." Tidus was vulnerable. A lot of guys, especially late-teens to early-twenties, sometimes put down perceived weakness in other men as a way of compensating for their own insecurities.

Edited to Add: As my profile pic may suggest, I also like Tidus. :)

I also really liked Conner Kenway from AC3.

Luke from Tales of the Abyss. Great MC with fantastic character development, going from being a bratty rich kid to someone who genuinely wants to save the world. Though I also think a lot of his detractors miss the point that he was basically a little kid mentally at the beginning of the game, so his awful attitude is at least somewhat justified.

Slippy Toad and Miles Tails Prower.

Max Payne. Fans seem to hate what Rockstar did with him in 3 by making him a depressive mess with an alcohol addiction. Although i love the first two games, i do think Max from 3 is the superior version of the character. His writing is superb and James Maccaffrey acting and delivery shines a lot more than before. He also gets a much wider character arc and development.

Raiden from MGS2. Though the fandom hate died down after 4 and Rising, there seems to be a consensus that his problem was not only the fact that he isn't Snake, but that he was a whiny bitch as well. I agree he can get annoying sometimes, but i think it's due to his character arc and he gets much better by the end.

Also agree on Tidus and Connor Kenway.

Squall “whatever” Leonheart from FFVIII.

Couldn't have said it better.

Also, not a protagonist, but I don't dislike Anise.

Zero from Drakengard 3, there was a change on the localization and they made her sound like she is angry all the time, however in the original japanese dub she was very calm (like she didnt care about anything that was going on), so she ended up with this rahter bitchy personality on the english version when in reality she isnt like that.

Here is a good video on the subject

Well i certainly dont have a poll to know how much she is liked over here, so im just going by my experience and so far ive seen a lot of people voice their hate towards her whenever someone starts talking about the game, it seemed like a trend so i imagined it may extrapolate in general, i may be wrong of course but since i have no data i just went with what i constantly saw.

John Cena.