Best theories I've heard:
1) Pegasi rely on their innate magic to do anything more than glide, and the "foal magic spurts" for pegasi manifest in higher-than-average flying ability
2) For the first year or so the wings grow faster than the rest of the body, then after that the wings grow slower until the end of puberty, meaning there's a period in life where NO pegasus can fly
3) Scootaloo is too busy crusading to practice flying

I thought this at first too but then realized,
poundcake weighs alot less and his wings are more ion scale with his body,
I've heard of some animals(mostly insects) that can fly when they're young but can't when they grow bigger,
once poundcake gets larger his wings willn't be able to support his weight and he will have to wait for his wings to grow in like Scootaloo is now