Warning: I talk explicitly about sex in this article. I assume that if you're old enough to deal with yaoi, you're old enough to deal with talking about the acts that happen in them. If you don't feel comfortable with that, now's your chance to go.
Yaoi is a genre that many people can enjoy for various reasons. However, there is one thing about the genre that I think some people don't realize: it's fantasy. It's not real. It does not reflect real life or real relationships any more than superheroes reflect real physics, and furthermore, it's not meant to.
Yaoi can be fun, but reading it as an instruction manual on men who have sex with men, or how relationships between them can work, is about as fruitful as reading steampunk to learn about history. Some of you may already know that. Great! You can go read something else. For those of you who perhaps are less aware of the differences, here are a few lessons.
1. Uke and seme are not roles set in stone.
A lot of yaoi has very clearly delineated rules of semes and ukes. The uke tends to be smaller, slighter, younger, more innocent or oblivious, and he also tends to be the one getting the penis stuck in him. The seme is larger, more aggressive, less emotive, and tends to be the one sticking the penis into something.
Some people may enjoy playing seme and uke roles in real-life, but many don't. If you think about it, it's actually pretty messed up to assume something as basic as appearance says something about your masculinity, your personality, and your sexual preferences. Height is just genetics and good nutrition; it doesn't say anything else about a person.
2. Rape should be left purely as a fantasy.
Don't ever assume that the kind of behavior that occurs in yaoi is okay in real life. When you grab someone who is sobbing, screaming, "No, no! Stop!" and have sex with them when it hasn't been carefully negotiated first, that's rape.
Rape or resistance fantasies can be played out safely for the fun of all players, but it involves an immense amount of trust, clear communication, and a way to bring everything to a halt before someone gets hurt. A lot of yaoi doesn't depict that kind of relationship. There is no communication over what's okay and what's not, the uke doesn't really have any way to communicate the difference between, "I am resisting and I want this" and "I am resisting and I don't want this," and as long as everyone comes in the end, it's portrayed as okay.
It's not. Erections and orgasms don't equal consent; a penis is not a rational entity capable of making decisions. People have to actually talk about it first and discuss what they are and aren't okay with.
Men have a reputation for being less communicative, but they are more than capable of sitting down and having an honest conversation about their preferences and limits in sex.
3. There are more kinds of sex than anal sex.
Yaoi is far from the only genre that assumes penetrative sex is the only "real" sex, but it's an obnoxious myth anyway. People have sex in all kinds of different ways, and queer men are no exception. Anal sex isn't the be-all, end-all of the universe. Some people love it, some people don't care for it, some people wouldn't do it if you paid them.
And that's okay. No form of sex is intrinsically better or more pleasurable than any other kind.
4. Sticking your dick in someone doesn't make you a Manly Man, or the Boss.
In a similar vein, if you do enjoy anal sex, it means jack all about gender role or how dominating or submissive you are. There are feminine women who like wearing strap-ons and using them on their happy macho boyfriends. There are people of all sorts of genders and gender expressions who like having sex their own special way.
On its own, sex is just an act; it's the people performing it who make it dominant or submissive, feminine or masculine. There are people who can be tied up, spanked, and still be completely, utterly the boss of everyone and everything. It's in the personality, not the parts.
5. Men are individuals.
This one might seem obvious. Of course men are individuals, right? It's not like they're all Manclones of the Manborg or something!
However, a lot of people will get caught up in whether Character X acts like "a man," and not whether he's actually acting like Character X! For some men, it's totally normal to cry easily; for others, it's not. Some men enjoy talking about their feelings; some would rather eat lava. People have far more differences as individuals as they do as genders.
So worry less about whether a character is properly "manly" or "yaoi" or not, and more about whether the character is consistent or not.
Yaoi can be something enjoyed by people of all genders and sexual orientations, but it's best to be mindful of what it portrays, and what it actually means. Think about yaoi and what it means for you, and also what it means to other people.