That's something that I've wondered about quite a bit. Not only can't you apparate in and out, you can't do it "on campus." Remember the apparation classes in HBP: Dumbledore had to remove the charm in the Great Hall during the class.
However, also note that the House Elves were able to apparate within Hogwarts.
Maybe it's because when a wizard aparates, he's casting a spell, which a Phoenix and House Elves are magical creatures, and apparation is part of what they are? Just a guess...
Man, I'd LOVE to have some HP conversations, especially today! I've been fighting IP routing and VPN fires last night between 6:00pm and midnight, and all day today!
Thank you. Forgotten about that. Being part of what they are (magical creatures) as an inate ability seems the most logical explanation. The Charm only affects spells, perhaps, as you said.