In this case, I think it all boils down to one thing: Deep down, these real archaeologists are just jealous of the Hollywood adventures of Indiana Jones and the fact that he's way cooler than they will ever be. Whether they admit it or not, most of the newer generations of archaeologists were first drawn to archaeology through those movies. (Take, for instance, the recent program on the History Channel that's all about just this idea, "Indiana Jones and the Ultimate Quest.") Once you get into "real" archaeology, the question becomes whether you're in it because you love the pursuit of knowledge about the human past or not. Trust me--those in it under a misguided idea that they're in for guns and adventure and hot pursuit by Nazis or Soviets are quickly weeded out. So grow up, boys, and face facts: Life is not Hollywood and the Indiana Jones adventures will always be more interesting to wide audiences than any of your books will ever be. (Burn!)
Jealous archaeologists aside, there is a segment to the Indy culture that takes a much different tone and is sure to please any history lover. Recently, the t.v. series that was released in the early '90s as The Young Indiana Jones Chronicles has been released on DVD in three volumes as The Adventures of Young Indiana Jones. These productions definitely do a better job of keeping to the known "facts" of history, and I think they're a fun way to explore the history of the early 20th century, so I can recommend them with a minimal disclaimer. If you're a history lover, you should check them out.
Also, if you're interested in learning where Speilberg and Lucas got this idea of crystal skulls, check out the articles at this link to Archaeology's website. As you'll learn, the reality is far from anything you'll ever see on the silver screen. Just like archaeology.