My understanding is that when cars got rid of the U shaped channel in the roof above the doors to improve aerodynamics, that left the rubber window seal as the only defense against leaks and it was never intended to be perfect which is why there are drain holes on the interiors of car doors to let water out. If you are seeing a lot of water, I would guess there is a gap where the seal isn't seating right up against the window as it should. You can also buy conditioning spray (I think it is silicone based) to spray on the seals to help keep them more flexible and provide a better seal.