Because it makes more logical sense. Not only does athleticism burn fat (which is the main component for breasts), but she'd be more aerodynamic with a more streamlined figure.
Also- given the incredible speeds at which she flies- the effect the g-forces would have on a set of large breasts would be rather damaging and unfortunate.
Fluttershy- on the flipside- rarely flies or does much in physically strenuous activity. Large breasts are also commonly associated with motherly figures- which one of Fluttershys stronger character traits.
Twilight, I agree. But fluttershy? She has to feed those orphaned (Mice, Bats, Bunnies, Bears, [Mammals of anykind] etc.) with something? She doesnt spend lots of time in ponyville, why? Shes shy, shy of people starong at her breasts. Pinkie, should be more chubby, and rarity needs the largest boobs. Cmon, spike cant just like her for two reasons. Applejack deserves rather large boobs, she is a workpony, she has the strength to carry em.