Do toggle bolts have to be perpendicular to the floor?
I can think of two things.  


When installing, being horizontal will help the wings unfold, as one of them isn't fighting gravity. 
Once installed, load is often in shear (meaning not straight-out, but at an angle downward).  If installed vertically, this will put much more load on the top wing of the toggle than the bottom wing, and it could be a "point load" which might help it dig into the backside of the wall in a non-desirable way.   If laid horizontally, the wings will see more of a pulling load, and be loaded evenly. 


However, it would be tricky to keep a toggle from turning as you install it, so I don't see any way a novice installer could control whether it's horizontal or vertical.