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As with every country, there are some rougher areas and less desireable areas to be in. Just remember to travel smart. We were in Bali while focusing on Ubuud and Nusa Dua and we felt completely safe. We hired a driver who was very good and I'm sure that also helped. I feel less safe in some areas back near home than I did in Indonesia. It's fine.
We didn't have a problem with crowds, crime, etc. mega hotels are there but if you don't like them, avoid them. If you go do typical tourista things, you'll find hoards of tourists, especially places that have regular tour buses, etc. there's something for everyone. We are more the boutique, off the beaten path travelers on a budget and we had a blast in Bali. We travel low key and don't bring flashy clothing, jewelry, or personal belongings with us.