First of all, airlines simply raised fares to cover the difference.
http://www.msnbc.msn.com/id/43883363/
Second, the taxes apply to the flight when you take it, not when you buy the tickets - it's essentially pre-paid. So people flying right now may be entitled to a refund because they pre-paid a tax that was allowed to expire.
The effect of this is that it is possible the taxes will be restored in a way that you will need to pay them when you travel. That is, the tax will be on your departure and will be due when you depart.
Stay tuned...