The problem isn't comparing homosexuality to pedophilia at all. If they are really compared for things they have in common. But that's not usually the case. However, homosexual advocates too often bash pedophiles instead on focusing on the flawed part. By which they support prejudices against pedophiles and allows others to criticize them for hypocrisy. For the argumentation: Well, if you can deny science and be prejudicial against someone, so we can.
The most common kind of argument is that if we allow marriages / sexual activities between the people of the same sex, we should allow marriages of adults with children or adult-child sexual activities. Of course trying you to reject both. And what you should spot it that it isn't about homosexuals and pedophiles in the first place. There isn't anywhere that it's only homosexuals who can do those things. You don't have to advocate legality of sexual activities between same sex couples, it's up to those who want to ban it to give a good reasons for that. And we don't only ban adult-child sex relationships for adults, who are pedophiles, but for all adults.
Do we have reasons for that? I think we do, children are generally less mature than adults. Marriage is a major legal act, we don't let children to make legal acts of similar severity. We know that with sexual activities there is a big risk of a significant harm for the child. And also children are less capable of defending themselves and it would be difficult spot those, who are just using the child for themselves without caring about the interests of the child, so setting an age of consent is also a tool to prevent that.
You can counter attack people, who use such argument, you can ask them, if they think adult-child sex relationships and child marriages aren't legal just because people think pedophiles are monsters, if they have no other reason for that. If they'd vote for allowing them if if there was a compelling evidence that pedophiles in general don't differ much or at all in personality from others and that they don't choose to be pedophiles.
Anyway, you can't argue that just because someone has a desire to do someone, they should be allowed to do that. The fact, that you have desires to do something doesn't give you a right to do that. Even small kids in the sandbox usually quickly finds out that they can't just take someone a toy because they want to play with it. But by the same principle you can't forbid someone doing something just because you don't like it.
And delete from your head things like homosexual are two grown ups. No, it doesn't matter how many people you have. It's about what sexual orientation they have. If you have a one person attracted to persons of the same sex on a bare island, it doesn't make the person any less homosexual. No pair of the following terms are equivalent: homosexual (person), homosexuality, same-sex sexual activities, same-sex marriage, same-sex sexual activities, sexual activities between homosexuals (there are heterosexual people who've engaged in same-sex sexual activities - it can be because of curiosity, because unavailability of the opposite sex person etc.), same-sex couples.