The UAV itself will have a computer running a commercial RTOS. The computer on the ground which the operator sits and and uses to interact with the UAV is almost certainly a Windows box. And as someone else said, the military's way of securing Windows machines like those has traditionally been not to hook them up to a network in the first place, instead of installing anti-virus software. That actually worked really well until portable USB devices came along. The result is that the military is only now getting up to speed on securing these types of computers; it's not that they're dumb about computers, it's that in the past they dealt with the threat operationally rather than technically.