A lot of guys like to run the woman's tummy, including myself. First of all most women's tummy is silky soft and it's so close to some of the best parts. It also shows a man that you trust them enough to be touching such a vulnerable area. And in the back of all men's minds we know what that tummy is capable of, and that is amazing.
Because when a guy likes you, he wants to touch you. And while he'd probably rather grab your boobs or butt, he knows that you might react negatively. Your stomach is safer, and if you let him, and even more if you like his hands on you, that may lead to more. That's what he's hoping anyway.
Now, if it's your BF, then he's just trying to hold and touch and comfort you without being overtly sexual.