Are frequent flier miles earned during official travel mine to keep and use?

You may keep frequent traveler benefits earned while on official travel for personal use, yes. (See, Public Law 107-107)

You can upgrade seating at your own personal expense – including by redeeming miles, for example.

However, official policy is that you may not select a travel service provider based on whether it provides frequent traveler benefits. Also keep in mind that a denied boarding benefit (for example, cash or a free ticket coupon) must be turned over to the government.