It depends on context. Imagine a couple arrange a date via a dating app (and have only seen photos and exchanged messages). When they meet in person, if one says to the other, "You're really photogenic!", that would be rude. It implies they look much better in photographs than in reality. But generally it's complimentary. Anyway, photogenic people tend to look good in person too in my experience :)

It’s complimentary but might be more subtle than commenting directly on someone’s appearance. If a man is talking with his wife and looking at a photograph of his wife’s sister, it might be more diplomatic to say “Your sister’s photogenic.” than to say “Your sister’s beautiful.”

"photogenic" just means that someone looks good in photographs, not that they don't look good in real life. As Claire points out, most photogenic people look good in real life also.

It just means that the person looks good in photographs. There is no negative or rude connotation. (Although sometimes any compliments are inappropriate, but that is a different matter.)

Wow, for me it's the opposite case. But, I've heared some people disagree with that kind of comments. Perhaps, it's a matter of culture due to our digital culture.