Pelosi's staff and family should not get these flights unless they are small in number, and accompanying Pelosi, but I think it is reasonable that the Speaker get a nonpublic (e.g., military) flight home, provided she pays at least what she would on an airline. It is certainly no more inappropriate than the military officers who take the little "military" business jets when traveling around the country. Remember that even as far back as the Lincoln assassination, we had a conspiracy to kill the whole top line of succession, from the losing side in the Civil War. The Islamo-fascists are motivated and capable of repeating this effort, and of figuring out Pelosi's quite regular flights home. We have to make it as difficult as possible for our enemies to target more than one such leader at a given time. Given the very public schedules of politicians, especially Bush and Cheney, it is helpful if their travel be secured from the public. This should not be a partisan issue. (But again, we should not be providing Pelosi with larger planes at taxpayer cost, so she can bring along others who are not in the succession.)
I think IRS regs says 3X the price of first class for "private" air transport.