We have rough in plumbing in the basement. We don't need a bathroom in the basement development. How should I cap off the toilet flange flush with the concrete to allow for flooring? Thanks.

You could fill it with concrete but this will lower the value of your home for future sale. I would stuff it with a wet terry towel allowing about a 2" recess left. Now fill that recess with mortar or quickset drywall compund mixed from a bag, not the paste stuff.