I doubt you will get an accurate reply. But anecdotally for me and my circle of friends, the majority of companies let the individual earn and keep their own frequent flier, or credit card miles/points.

The (minority) remainder of the companies, on the FFP side, have negotiated special non-mileage-accruing rates with the airlines. And on the credit card points side, require individuals to charge all business expenses to company-issued cards.