The miles that were earned during company travel belong to the company.
In today's competitive market most companies allow the employee to keep these miles. As the market for airfares, unemployment, etc.changes, I could see that changing.
Time on airplane, away from home, etc. are apparently part of the job you accepted.
Nevertheless, the company can demand for you to use the miles that were earned with the company's money (for both airfare and your salary). You can chose not to do it, (just, as an example, you can chose to take unapproved vacation). I do not know what your company will do [if anything] to reprimand you.
I do not like it, but I repeat: technically the you received the miles from airfare and salary the company paid you.