>Brains perfectly work rationally while horny

Completely untrue, rational thinking can be impacted by all sorts of things. You don't have to be intoxicated to have a lapse in judgment, being hungry alone is enough to make the smartest brains slow down.

As for your original question, 1) folks don't really think rationally when your brain expects pleasure, you just want it and don't have time or resources to ponder the ramifications like you would any other time, 2) people like sex better without a piece of latex getting in the way, so some deliberately choose to take the risk.