Technically Dany doesn't know what he looks like either. I assume they could easily tell the audience via some basic exposition. Like Dany seeing the image and going "...who is that...Rhaegar?" or something to that effect. Plus there's a certain family resemblance most Targs have that would make it a bit more clear as well.Conor, yeah I hope Rhaegar shows up in Season 2, since I really don't see him appearing this season unfortunately. There's also that scene in Clash of Kings where Dany has the dream/hallucinogenic trip experience in the Houses of the Undying. She sees Rhaegar there, but they may not show that on TV because, if Rhaegar hasn't already been introduced, the audience wouldn't have a clue who he was.
Seeing Robert & Rhaegar battling at the Trident would be effing awesome!