First off, with the exception of my kitchen and bathrooms (slate) all flooring in my house is wood - local spruce planking in living room and bedrooms and chery in dining room. None of my floors are painted but I did consider it for my young sons bedroom. Yes, wood can be beautiful by itself but why not consider painting it to achieve a different look. I have seen many old homes that have painted plank floors and they look beautiful. I have also seen brand new houses with oak floors that have absolutely no character whatsoever. Maple in my view, unless you get some nice birds eye, is pretty bland. Poplar is what I call a great imitator in that it can be made to look like any wood with the proper stain. By itself it would be quite boring as a flooring.
I think that you should not feel almost "dirty" because you entertained the thought of painting over natural wood. Heck, I just dark stained all the pine clapboard on my house without a second thought.
I also do a lot of woodworking and generally leave the wood in its natural state but that's not to say that I am afraid or ashamed to paint over the grain of the wood.
Who knows, when he gets bored of the color of his floor maybe my son would like to make a change by painting - and I may very well let him go ahead and do it.
Hey, its a floor! You walk on it, you drop things on it, its gets dented. Whether dented, or painted or left natural, its still a floor and its there for walking on. If the paint wears thin in a few years - paint it.
We wanted an old looking floor. I put down spruce plank. We have two young children (3 and 1) who are now in the process of "quick aging" our floor. Its dented, its scratched, there are gaps in the winter. Basically it looks old - which is what we wanted. Others may not like it - especially in a three year old house - but we do. And that's what matters.
So, Red. If your wife wants a painted floor and you have no problems, then go right ahead.