Trying to directly cap emissions seems like a good way to make the program fail before it even starts. Do you penalize fliers who end up on an older, less efficient jet? Takeoffs burn a lot of fuel so do you penalize fliers who take flights with a layover? If a plane flies half-full, do the passengers pay more?
Capping and trading is the more simple solution. Instead of putting various restrictions and limits on a ad hoc basis (often influenced by lobbyists and special interest groups) for dozens and dozens of activities, you have just one unified system.
I also think it would be an easier thing to sell politically. Most people don't fly every year and giving them an easy way to turn their lack of travel into a small bonus is appealing.
A cap-and-trade program has the double whammy of being a tax / regulation and pro-environment. Two things the right and much of the center are going to say "no" to.
It seems like a practical implementation of a bonus-malus system.