The difference is the knowledge, consent, and support of the governments involved. Terrorists can operate pretty freely in the US, Canada, Germany, etc., because they are, by and large, free societies, not because they share the terrorists goals. That is different than, for example, Egypt, Syria, and Afghanistan who at best turn a blind eye to the terrorist activities and at worst provide direct assistance to them.
If terrorist operations are discovered in non-consenting countries, the method for acting against them is different -- it essentially becomes a local problem, though any information obtained would be wanted by the US, and likely given to them. Military strikes are not needed when the local governments are taking care of the problems themselves. Take, for example, the aggressive crackdown on terrorist cells in the US, Canada, and western Europe over the last couple of weeks (it is likely that many of them were under surveillance (but not enough evidence to act against) prior to the WTC/Pentagon attacks, and those were then likely the starting point for rounding up what can be uncovered) -- in these "friendly" (cooperative governments) areas, it is more like policework, as opposed to the "unfriendly" areas, which will require covert and/or overt military action.
As I said in my earlier post, there are a wide variety of methods available, and it comes down to choosing the correct mix of those methods for each particular case. Obviously direct military action is appropriate in some cases, and would be absolutely wrong in others. The same could be said for the other methods as well.
The US supported the KLA and Chechen terrorists. Many muslim countries are openly on the side of the KLA and Chechen terrorists too. Bomb Washington?