I have a policy like this for my small consulting company (with only 3-5 traveling employees each year) where the matter is one that I presented to the employees and explained my reasoning.

The options were essentially for employees to keep their own miles, but that the company travel policy would essentially require travel on the lowest fare regardless of airline. Alternatively, the company would commit to keeping them on a specific alliance as far as possible to allow them to earn the perks of elite status, but that we would reserve the right to use about 80% of the miles earned for business trips when needed. The savings we realized from using miles in lieu of our travel budget would be plowed into a pool, part of which would be distributed among the employees at the end of each year as an incentive/bonus.

The employees unanimously chose to adopt my suggestion and we've been using it for 3 years now without any gripes. Of course, if an individual client project has their own travel policy then we defer to that, but I try to negotiate most of our fees on a per-project basis (inc. travel budgets) so we have more control of costs.