"Maybe the people who hate paedophiles are secret child molesters?"
There's no evidence for that, no.
There does, on the other hand, seem to be a remarkably high number of people (like Ted Haggard and numerous American and British politicians, public figures and religious leaders) who publicly declare that homosexuality is sinful etc., and then get caught out doing it themselves. Plus some studies like this indicate that some homophobes (not all) do feel same sex attractions.
So the evidence does differentiate the two statements a little bit.