Before you commit, buy a small piece of each wood, stain it the color you're thinking of using, and see what you think. If you like how they look together, go for it. If not, change your plans. It looks best if the wood work together, but it's your house so go with what appeals to you.

That sounds good to me; however, if you ever want to sell the house it may turn off others.

Are you saying you're using different species? or the names of the stain colors?
You didn't indicate any details re: the "floors" are that you're trying to tie in with...

Colors, &/or species don't necessarily have to "match"... but they should definitely have a common denominator which allows them to compliment one another... not clash.
But what do I know... I do floors... lol

The floors and the window trim are a natural white oak so they match . My question is, s it ok to do darker doors?

White oak is neutral and will pretty much match anything. Do a test sample first.