So do you want the government to have a searchable database of all the flights taken?
If the airlines have to keep it, and the government can draw from it without a public warrant, the government is keeping the data.
Do you want Joey cop on the block to know how often you fly out of the country? Do you want all your daughter's travels available to any LEO that is interested? When you say yes to the first, you are saying yes to all of them.
I believe the [federal] government (FAA, FBI, etc.) has had access to flight passenger lists for a long time, so maybe what they are requesting now is more easier and real time access to the data or perhaps broadening the scope of how the data can be used. For most people, travel by flight accounts for only a small fraction of their activity - maybe one flight a year.
I'm actually more concerned about the government having access to stuff like Google Maps history and other geo-location data coming from our smart phones.
"Do not seek to follow in the footsteps of the wise. Instead, seek what they sought." - Matsuo Basho