Optics quality being the same, the answer is yes - but only if the magnification is high enough to warrant it.
For example: If you have a 50mm scope set at 10x, then the exit pupil is 50/10=5mm. If you have a 40mm scope, you can achieve 5mm at 8x. If you have a 40mm scope and you set it at 10x, then the exit pupil is 40/10 = 4mm.
The human pupil opens usually no more than about 4mm or so, which means that you can use a 40mm scope and set it at 10x to get pretty much the most that your eye can use anyway.
Now, if you have a 50mm scope and for some reason you want to crank it up to about 14x, then you will have an exit pupil of 50/14=3.57mm. If it was a 40mm scope, then it would be 40/14=2.85mm. That means that a 50mm scope would give you a greater pupil size at 14x, and thus more light to your eye. However, how often is it that you will be using a scope at 14x? Not often. Not even for coyote hunting, but if you need to, then a 50mm would be more "useful."
Now, that said, I also like 50mm scopes for another reason - eye alignment. Just because an exit pupil may be more than 4mm doesn't mean that it is a complete waste. Rather, if you exit pupil is say 4mm, but the scope at a particular setting gives you, say 6mm, then it is easier for your eyes to align with the scope.
Again, it all depends on what magnification you use. The bottom line is it is much better to get a 40mm scope with high quality glass, than it is to get a 50mm scope with cheaper quality glass.
Zachary