I agree with Aralith, it's just the way the character is. Cloud is a very weak character, and some of the more macho players out there simply don't gel with that very well. Some could very well not like him for the fact he always seems to be in another emo crisis.
But another thing that a lot of people won't like the character for, is the fans of the character. There's some rabid fan out there. I recall seeing somewhere on these forums (a looooooooong time ago) someone posted saying that they "loved Cloud. Really." While such a thing simply makes me lmao, others it would really tick off. It just irks them. And for that, the character is bashed to kingdom come.

There's nothing you can do about it, really. A similar situation can be seen in the LT of FF7. A majority of the Cleriths hate Tifa and a majority of the Cloti's hate Aeris. Not necessarily because of the characters, but because of those that support the opposing view. As a way to lash out, they attack the character.