I'm not sure how the regulations for US personnel are applied. In Australia, there used to be some discretion at a unit level for commanders to approve travel on a case-by-case basis. Visiting family, in a major city, would likely be interpreted positively.
As an American citizen, you are automatically considered to be a 'higher value target' (for those who look for such targets). As an American serviceman (on active duty), increase that 'value' by a factor of 10 (or some other arbitrary number).
Still, the likelihood of running into trouble is very remote, particularly if your son has lived in Indonesia for a while (he'd know what to avoid). His awareness of such things will likely be reinforced by his training there too.
If visiting Indonesia does become a problem, you could always mitigate this by meeting in a third country (Singapore springs to mind) and bypass the issue. That might work for immediate family (parents and siblings), but could be harder for a large extended family (aunts, uncles and cousins) and friends.
It'll also be affected by where he's eventually posted (given the vast network of facilities the US maintains). While likely stateside, overseas is an eventual possibility. You could turn a visit into a family holiday, wherever he ends up.