Unity uses Y as up (if I recall correctly)
It's not irrelevant to what the renderer uses. If you draw a polygon on your flat screen and increasing the Y value making it go higher, you'd think that, well, if that's how the renderer did it, maybe I should just follow the same pattern and make my game engine like that?
Also, I'm pretty sure in my calc 3 (what ever I had before diff eq) we used Y as up but I could go look at my old notes if necessary.
Blender uses Z as up. Blockland uses Z as up. Garry's Mod uses Z as up.
Honestly, the names are just about as important as colors. Z being blue, Y being green, and Z being red. They can be whatever the hell you want to call them (or color them as I tried to make the point of). I could make my axis DOG CAT and TRAIN and it wouldn't make a difference (well, maybe syntactically but not semantically).
And MANY games and engines have an axis of Y being up. Just like there is no standard to which horizontal axis becomes North/South and East/West.
Also something from gamedev.stackexchange on the matter
http://gamedev.stackexchange.com/questions/46225/why-is-y-up-in-many-games