I hate to break this to you, but Indiana Jones is a FICTIONAL character. While media certainly influences our perceptions of reality (art imitates life) we must be reminded of the fact that entertainment is about entertaining, not educating. This isn't to say that film cannot be used for educational purposes or for creating awareness, because it is a powerful tool for such endeavors. There are many things that film teaches extremely well and movies have been powerful tools for exposed people to issues and topics. However, one must approach the Indiana Jones franchise with a healthy suspension of disbelief in order to realistically categorize the material for what it is.
Indiana Jones is really less of an archaeologist, and more of an adventurer. The movies are about a character who encounters unique and extreme situations that are loosely related to archeology. Of course it doesn't hurt that for the sake of entertainment he encounters these unique and extreme situations on a semi-regular basis. What is interesting about this topic is that in the third film, "Indiana Jones and the Last Crusade", Dr. Jones is actually addressing this topic. He is lecturing to his university class and he talks about how the majority of archeology is about spending time in the library doing research. In addition, he states that "X" never marks the spot. Granted, later in the film "X" actually does mark the spot, but it wouldn't be a movie if it didn't, right?
The positive side effect for archeology is that the Indiana Jones franchise has an opportunity to create interest in the field. Granted, it does require people to make an adjustment regarding the reality of what the field actually entails, but exposure to history and historical artifacts in any form can be beneficial for creating intrigue. As with many things, measuring the "good" or "bad" of something is all about evaluating what it actually is. If you are watching Indiana Jones and viewing it as a documentary of archaeological behavior, you may be disappointed. Try some popcorn instead and enjoy the movies.