Lots of US citizens hold passports from other countries. I have friends that have both a US passport, and a passport from Israel, Canada, New Zealand, Australia or Ireland (they have a US passport and one from those other countries - more than one friend). The only thing you have to remember is to use the same passport on entering another country and returning to the US, or things can get quite sticky.
So Obama used his Indonesian passport for what reason? To get better treatment by “proving” he was a Muslim, too?