I dont think it necessarily has to run in the family, but, when two people with abilities have a child, that child has a much high chance of developing powers, though, it doesnt seem to be consistent, the powers are random, no two people that we know of, have the same power (not counting peters or sylars ability to take powers from others)
lets see, so far we got
walking through walls + multiple personality/she hulk lol = techno path
fling man + pyro/fire starter = regeneration
although, in the case of Nathan and Peter, it is possible that one or both of they parents have a power, I mean, what are the odds of those two having powers, out of all the (what was it something like 36?) people around the country/world on the list, being brothers
it might be revealed that they father had a power at some point, maybe even they mom, who knows