We can not be sure if all part of Indonesia is dangerous. And it is pretty sure that in all over the world there is always a small possible dangerous thing to happen, including small traffic accident or stomach ache if you eat hot-spices food. But, I believe that Indonesia in general still a save place to visit.
If you feel that your people become target of terrorist as many expert - and your government - believed to be so, then I strongly recommend you not to visit and hang around the most common tourist site, such as famous beaches, big hotels and cafes, as well as malls and shopping centers. Instead, you should come, visit and enjoy our local people as well as their traditional activities. By doing this, you are not only able to witness how peaceful Indonesia is but also helping more Indonesian with their business.
Try to get information from local airport staff or taxi driver on any cheap but decent motels or cottages which close to local community. Visit their traditional markets and interact with them. I can guarantee you will get the most peaceful and friendship welcoming atmosphere from Indonesian people - children, youth, worker class group and elderly - on your visit to Indonesia.
If you do follow my suggestion, I can guarantee you that Indonesia is not as dangerous as you and your government think of. And if you really at the end visit Indonesia, I believe you will find out that Indonesia is a beautiful country with kind and great people who will always love peace and friendship with every people from around the world. So, don't be afraid, mate! You will be save.