The hardest hit area in Indonesia is in the Banda Aceh area (northern tip of the Sumatra Island). The separatists in Aceh have been fighting against the Indonesian government for autonomy for quite time. The civil war got so bad that the Indonesian government pretty much sealed up the Aceh area even prior the earthquake and tsunami (i.e., no foreign journalist, no tourists, special permission required, etc).
I believe the Indonesian are grateful for any help. However, they have a dilemma as they are concerned about the safety of the foreign relief troops in this area (not just US troops), that is, fear of being attacked by the separatists. Imagine the U.S. inadvertently getting embroiled in a civil war:
http://story.news.yahoo.com/news?tmpl=story&cid=574&e=11&u=/nm/20050113/wl_nm/quake_dc_286
The good news is...just heard in the news...the separatists are calling a ceasefire with the Indonesian govt to allow relief work to occur safely.
P/S.
The same situation is happening in Sri Lanka....there has been a civil war between the indigenous Sri Lankans (primarily Buddhists) and the Tamils (primarily Hindus). The tsunami tragedy is causing a bit of dilemma for the govt and relief agencies in distributing aid.