No, Indiana Jones is not bad for archeology. In fact, I'm sure that a lot of people with an active interest in archeology and related anthropology fields were at least partially influenced by this series. While the Indiana Jones movies represent a Hollywood version of archeology that's more full of adventure than real life, they make archeology "cool".
Speaking for myself, I can actually remember wanting to be an archaeologist as a young kid. It was always trying to find something to dig up or searching woods and beaches nearby for interesting finds. While I never found anything that dramatic, the search in and of itself was much fun.
In fact, I can largely attribute my early interest in archeology to watching the Indiana Jones movies. A popular movie series can definitely make science look more fun than reading about it out of a book typically can.
While movies can paint a somewhat inaccurate view of what archeology is really about, they can definitely help to bring out into the mainstream. After all, how many average people would give much thought to the Ark of the Covenant if there hadn't been a movie made about finding it?
Also worth noting is that the subjects of the first three Indiana Jones movies and the coming fourth one are based on real artifacts or well-known legends. Seeing a movie about any of these things will arouse most peoples' curiosity.
The Ark of the Covenant, written about extensively in the Book of Exodus and mentioned throughout the Hebrew Scriptures, is one of the biggest historical mysteries there is. This was the subject of "Raiders of the Lost Ark" Often thought to have disappeared when the Babylonians destroyed Solomon's Temple, its current location is still unknown. Theories range from being buried deep under Jerusalem to being located in Ethiopia (commonly believed to be where the Queen of Sheba hailed from).
While the Kali-worship featured in "Temple of Doom" is fictitious, there are cults known in history that have taken part in terrifying rituals that bring this movie to mind. One such group, the Chavin of South America, were featured on a "Digging for the Truth" episode titled "The Real Temple of Doom" (http://www.tv.com/digging-for-the-truth/the-real-temple-of-doom/episode/630444/summary.html). The Chavin were known for using hallucinogenics as part of their rituals, possibly leading to mass mind control.
The "Holy Grail" (subject of The Last Crusade) has been the subject of hotly-debated legends. While there is no Biblical evidence that the chalice used at the Last Supper was venerated by early Christians, many legends have sprung up inspired by it. The Grail legend is prominent among some Celtic Christians.
The crystal skulls, featured in "The Kingdom of the Crystal Skulls", are also part of debated legends. Scientists are unsure of whether they're ancient Mayan artifacts or actually more recently created. In either case, they're an interesting group of artifacts to study.
While fictionalized, the Indiana Jones movies do make archeology more popular and generate interest in some of archeology's most fascinating mysteries.