I don't have a problem with this. Lots of VIP's fly on military aircraft -- from the first lady to high-ranking military leaders. The speaker of the house needs to have good communications with Washington at all times, so it makes sense to travel on military planes. It was only when she requested a 757 that I thought she went too far.
The Speaker wasn't issued a military plane until after 9/11. It's a waste of resources, always has been and always will be.