I had the same thing happen: Some friends who bashed Crystal Skull also loved not only "Transformers" 2, but "G.I. Joe" as well (I place them in quotation marks because they are not those properties, save in name only).
I had to ask them why.
They said it's "okay" for "TF" and "Joe" to be silly, stupid and all that because they were based on toys. Okay, I said, but why then hate Indy IV? Raiders was never intended to be anything other than a silly, stupid serial, the 1930s equivalent of being based on a toy. Well, immediately they dug in their heels and started sputtering about how Indy was great. And, yeah, I'm in agreement. Indy IS great. But I think the concepts and original design of Transformers and G.I. Joe are great too, and *their* movies didn't live up to them.
I really don't understand why people bash one movie by the same criteria with which they praise another. Personally, I loved Crystal Skull (and hated "TF2" and "Joe", by the way, because they DIDN'T try to be what they should have been).
I think those who bash Crystal Skull are mainly those who worship the earlier films with the same simple-minded approach with which humans worship most anything else: They enjoyed it as a kid (or had a kid-like mentality), so age makes it better, etc. They're defending a simpler, more comfortable view of the world which new data and new analysis' intrudes upon. But when one looks at things objectively, Crystal Skull really isn't any different than Temple or Crusade. I think "Raiders" is a bit different (more serious, Indy talks less, he means more business, and the McGuffin is feared rather than coveted), but they're all approached the same and done well.
I bet if Crystal Skull was made first, those same people would bash Raiders itself because it introduced religious themes when Indy is "supposed" to chase after ancient aliens.
Some people . . . seesh.