It's called blotching and is normal for cherry, especially when using an oil based stain on bare cherry.
I don't have any experience finishing hardwood flooring, but I do have experience finishing cherry furniture.
If I was finishing cherry furniture I would apply a 1lb cut of dewaxed shellac, and when dry, lightly sand it with 320 grit. Then I would apply a gel stain, and only do a small section at a time, where you can wipe off the excess gel stain after three minutes. Wait too long to wipe off the excess and you'll have a sticky mess. After at least 24 hours of drying, I would apply the clear finish.
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