At the end of PS/SS Hermione says: "It's strange to be going home, isn't it?"

Then Harry says (looking back at Hogwarts): "I'm not really going home".

Then I realised in OotP or HPB (i can't remember which one), Dumbledore says that Harry would stay protected as by Lily's love as long as he could call Aunt Petunia's house home. When he says I'm not really going home, I think he means he thinks og Hogwarts as his home.

that would mean he wouldn't be protected if he was calling hogwarts his home.... would he???

P.S: He also says that Hogwarts is his home to Dobby in CoS!

Well, he may not consider it his home, but because of the charms that DD put on the house when Harry was a baby, as long as he can return there for part of the summer, in the home where his Mother's blood protects him, then he will be protected by that magic that his mother protected him with. He may not consider it home, but he is still allowed to return there every summer, and he has to for the protection to continue. He does want to stay at Hogwarts over the summer in the book, but DD tells him he cannot. He only has to return to Privet Dr. once a year for the spell to continue to work, and as long as he does that and stays for at least a month then he is safe to go to the Burrow, or other places the rest of the summer. The charms only work as long as he is allowed to return there once a year before he turns 17, so he really doesn't have to call it home, but they can't kick him out or he will not be protected. That is what Petunia knows, and what the howler in OOTP reminds her, because she was close to kicking him out after they thought he harmed Dudley.

Yep, what Potterwatch said. Also, the protection lasts as long as he "can call" it home. He doesn't have to, but as long as he can (in other words, as long as he can return there every summer), the protection lasts. And it obviously did, because ... well, that's how the story goes. There's not much point in looking for non-existent plot holes, in my opinion. That part of the story, at least, flows quite nicely.