Well, basically there is no reason against flying in green. However, it's easy to differentiate the colors. And since R&D likes to reprint the same stuff over and over again, so they reprint green hate vs. flying over and over.
Every other color has more or less useful tools against flying. Red has burn, black has
Terror 
, blue has flyer and white has flyer and removal. But green? Well, since green is designed as a stupid, P/T centric color, it's rather a necessity to print some hate cards vs. flyer.
But this doesn't solve the problems for other evasive abilities like fear, intimidate, unblockable, etc. There you have the same problems with green. Every other color can do something about it, but green is just too stupid.
There was a long discussion a few years ago and I mentioned the green uselessness against a
Peacekeeper 
. Such a creature could stop green totally. Back then, I suggested to print an ability more often that should be similar to
Gargantuan Gorilla 
... and maybe even keyword it just to replace provoke a bit.... and right now, we have "fight".
It's a great tool for green against any control creature that wouldn't block or even denies attacks completely (see
Magus of the Moat 
). All those
Plummet 
spells are completely useless in this case.
Whenever I design cards, green usually has some flying creatures. Flying should be a general keyword every color should be able to use.
I gave Green more archery effects (like
Elite Archers 
). Unlike the current green archery, it isn't limited to shooting down flying creatures. Basically, it's the green form of first strike. It's fantastic to stop creatures with intimidate as well. Green also got spells that do similar things.
In my "universe", the color with the least flyers is black. Basically this comes by the fact that for me, black is more a subterranean color. So it gets
Crawlspace 
,
Gravity Well 
, etc. Even demons do usually have other forms of evasion (f.e. protection from cmc3 or less || or
Demoralize 
).
In addition, Green got lifelink from white (since white got bounce and other stuff). In this way, it's garantueed that green can take the leading role and simply attack each turn.
So basically, next to archery, lifelink and fight, I have no space for such stupid things like fyling-hate in Green.
