I am a small business owner in a very travel-intensive business--trade shows. I also teach a course entitled
"Frequent Flyer Programs--Payback Time for the Trade Show Road Warrior" which is attended by many trade show/exhibit managers from all sorts of companies within my industry.
From teaching the course I have learned that almost all companies allow traveling employees to use their actual flight miles as they choose. The only exception I have heard of is the Federal Government which allows the employee to keep the miles but to use them only for upgrades not FREE tickets.
Many exhibit managers (especially in the High-Tech field) are also able to keep all the points that accrue to their AMEX cards as a result of shipping, drayage and labor associate with their company's booths. This can be a very serious $$$$$$$ amount.

This privilege does not, however extend to people who work for large companies that hold government contracts.
In my own company all employees are allowed to keep their own airline miles and use them as they wish. I even coach them on how to make the most of their travel and will help them figure out how to attain status, fly first class, etc. The credit card miles for purchasing their tickets, however, go to the company. Fair enough--win/win.
Business travel is extremely brutal and the miles and points an employee earns are a small token we, as employers, can offer for their committment, dedication and service to our companies. I even reward them and their spouses with special trips on my miles and points to let them know how important they are to me. I can't imagine handling it any other way.