It seems ever since the movies were first released, the idea of Frodo and Sam being gay has been around. I do think it's just a joke and most don't take it seriously, but still, after awhile it can be quite sickening.
As mentioned, I think this mostly comes from the idea that the true male hero is supposed to "manly," meaning they cannot show any sort of emotion or affection. I hate the fact that in this day and age, people automatically assume that a man's love for another man can only be sexual. Men aren't robots- they're human. I appreciate that PJ kept the characters' affections for each other in the movies. For this, perhaps the relationships (another automatic assumption these days- that relationships are always romantic- no, friendships are relationships too) shown in the films are more realistic and human than most films you see in theatres today. Most films don't show that sort of affection, and it influences our culture. Maybe if more movies showed the type of love between characters that is seen in LotR, then relationships between Sam and Frodo and Aragorn and Legolas wouldn't be perceived as gay.
The problem is that in our society, homosexuality has become so frowned down upon. Straight males don't want to be misinterpreted as gay, so it's important for them to stick to their "manly" behavior. I noticed in my high school, many guys would joke about homosexuality...sometimes they would go as far as imitating gay males. How would they do this? By hugging each other (apparently if one male hugs another male, they're gay

) and slapping each other's butts. Joking around and commenting that Sam and Frodo are so obviously gay is similar to that. Most people joke about this simply because they are uncomfortable with the subject of homosexuality. It's their own problem and they need to get over it.
That said, I've been lucky enough not to deal with most of those problems for the last few months. A large percentage of my school is gay, so most students understand the line between what's just friendship and what's sexual. No one is uncomfortable about homosexuality, therefore jokes don't need to be made about it. Then again, I think the straight males at my school often feel the need to be extra "manly" because it is extremely easy for them to be misinterpreted as gay...