Without being able to see it I'm thinking that you need to call your vet and discuss it with him/her.
Do make sure he's on clean bedding. I'm assuming you've cleaned around the penis to see if there is a cut or obvious wound? Is it bleeding continually or just a little?
If you have trouble holding a rabbit that has an injury (because he's kicking around) you can gently wrap him up in a towel and just open up enough area to get to the injured part. I would keep his head out of the towel so he can see unless he still freaks then try hiding his eyes too.