This is something I've always wondered, along with Pokemon that can surf. Now granted this is a video game and we shouldn't really question it's logic, especially when it's Pokemon of all franchises, but I often find it weird that it's possible for someone like a heavyweight boxing champion, let alone a 10 year old boy could ride on top of something as small as a Pidgey.
Granted they could hold the trainer in their talons like how an eagle would catch it's prey, though that could possibly tear the trainer's clothing unless it was made of a special material. I personally find it cooler to ride on top of the Pokemon rather than it picking me up.