Sometimes I wear cargo shorts (I know.... they do catch the wind). When I do, I make sure to wear something like UnderArmor underwear briefs underneath. The synthetic underwear has to be tight enough not to move around ON YOU. It also should be wicking, so as not to absorb and hold moisture, which can also cause problems.

Don't get on your bike with only your normal cotton shorts, unless it is for something like a short or leisurely paced fun ride.
edit: Your undershorts should be akin to a second skin, without being uncomfortably restrictive.