How safe are the southern Philippines?

Attention: I write this in english but chosed Filipino (Tagalog) so that maybe enough people from the Philippines find this entry and give me some answers.

First to me the Philippines are such a beautiful country altough I never was there I'm planning to have vacation there in maybe a few years. Because I do not like the big crowded cities like Manila I would more like to visit the south including the city of Zamboanga.

But surfing through the internet I unfortunately found out that Zamboanga is the main city on an island which the Abu Sajjaf demands to be their territory. If you don't know: The Abu Sajjaf is a extreme fanatic muslim group you can compare with Al Quaida. Their goal is to build a muslim state in the southern Philippines. They are very violent and dangerous and are counted as a terrorist organisation.

Also I read that the Philippines have, due to their massive number of islands, many problems with pirates patrolling on small selfmade boats looking out for ships where they think rich tourists are maybe on them they can rob. How safe it is there to travel from island to island without aearial transport (cause I think many small islands do not have a airport)?

I'm really not against weapons and I have no problem to survive in a country which is more dangerous then mine because Berlin is a very harsh city especially in night. But the Philippines with all their jungle which you can't see through and all the small islands where you do not know whats hiding there scare me a little.

Also how about the criminality there? I think tourists are robbed very often especially when the people see that you have white skin because then they think you must have a lot of money (which is to me nothing more then racism).

Do not understand me wrong. I really like the Philippines very much and of course I would make there vacation anyway but I just want to see the experience of some people from the Philippines.

Ah and how about medicine? Do I need to take some inoculation before I can fly there? If yes what are the sicknesses I need to get a inoculation against to?

Thank you all so much!