One strains to find a profession or science that Hollywood has not glamorized or attempted to make sexy. In most films and TV shows, the focus is not necessarily on getting things right, but on making it look cool. Does this have an effect on the way people perceive these professions? Perhaps. Is it bad for those professions? Not really. Indiana Jones is a perfect example of a profession and a science being misrepresented to a wide audience of popcorn inhaling viewers. He is not the real thing, but a Hollywood facsimile of an Archaeologist who experiences danger at every turn, sees exotic locales and beautiful women and comes out on top in the end. But is he bad for the profession? Probably no more so than Jack McCoy (of Law and Order) is for the legal profession. In the end, his fictional presence is certainly no disaster for the field.
What is the greatest danger a modern archaeologist may face in the field? Probably getting drunk and falling into a ten foot deep excavation unit, or more realistically, landing on your trowel. The Indiana Jones films may leave people with the impression that archaeology is a field rife with danger, when in fact danger in archaeology is rare. But who can deny that there may be a place or two wherein digging for old pottery may actually be dangerous?
One could be leading an expedition into a less-than-stable region of Africa, or into a place where the locals aren't particularly friendly to folks from your country of origin. It deserves stressing that this is the rarity, but then Jones points that out in the films himself! "This site also demonstrates one of the great dangers of archeology, not to life and limb, although that does sometimes take place, I'm talking about folklore" (Raiders of the Lost Ark). As if breaking the fourth wall, there is acknowledgment that the situations we see him are not the norm.
As with many cinematic forays into exotic locations, the films may have caused controversy among populations depicted in the films. Although it certainly isn't something we ought to dismiss too lightly it is exceedingly common for Hollywood to offend. However, even given the controversy that may surround the film, the real field has caused controversy itself! It has to be expected that a people or two may take offense when you go to dig into their people's ancient grounds. Furthermore, archaeological findings can stir controversy. An anthropological/archaeological discovery in the Midwest United State seemed to link several Native American cultures with cannibalism. Naturally there was some dissatisfaction expressed with the findings. But controversies such as this come about regardless of the existence of Indiana Jones, and really any offensive depiction in a film reflect more on Hollywood. Indy's actions are what really may reflect on archaeologists.
This is what raises the question of Jones' methods, or apparent lack of them. His search for historical artifacts is often marked by irresponsible actions and only half thought out decisions. Here, however, it is up the viewer to remember the context (one of the most important words in the archaeological vocabulary). Jones has Nazis breathing down his neck at just about every turn and time is of the utmost importance. In reality, the nearest deadlines are likely those associated with the extent of funding, or when the construction company is going to flatten your working area and lay concrete. No one is about to shoot you to steal your work and use it for absolutely nefarious deeds. Given the context and Jones own words, the viewer can see that the way in which things are getting done under Jones' watch are not the normal day in the life of an archaeologist. This is the fictional and stylized world of Indiana Jones and chances are that the same people who need to be told Jones isn't real, are the same people who would simply call archaeology grave robbing even without the films to influence them.
Of course, like many fields of research, archaeology can be connected to a lunatic or two who have either gone off on their own and conducted their pseudoscience, or released their own ludicrous "findings" as fact. This is a fact as best put by Robert L.Bettinger:
"Science, and especially archaeology, is always going to be plagued by crackpots and crackpot hypotheses. That's because science makes room- in essence, provides a "niche"- for any hypothesis, no matter how silly. Indeed, it is progress in knowledge, evidence, and understanding that separates plausible hypotheses from the silly ones which are completely abandoned and pass from scientific consciousness... Thus the more archaeology progresses in its pursuit of plausible hypotheses, the more it invites challenges from the lunatic fringe. It's just a cost of doing business."
The field of archaeology, like other fields, has a structure in place to weed out those that do not belong. In education, there are 100 level courses where someone might find that this isn't the field they expected, and there are professors to teach them the real methods used in the pursuit of fact. In the field, there is the natural difficulty of finding and reaching good sites. Erroneous findings are eliminated through peer review and fact checking. There will always be people who would get in the way, of course. There always have been, and always will be looters, there will always be people who have the wrong ideas. But these people existed before, and always would have even if Harrison Ford had never donned the fedora or cracked the bull whip. In short, Indiana Jones is not bad for the field of archaeology, because the field of archaeology is capable of dealing with the existence of a would-be Indiana Jones.