I dont use PAI, but lookin at their 'official files', they have  a 'FS2002 Special Package' that will remove your default commercial flights. Maybe thats what your lookin for.

There are manual ways as well using TTools.

You could edit the decompiled 'flightplans.txt' file, removing the unwanted flights. A daunting task, to say the least.  

Or, a better choice, edit the decompiled 'aircraft.txt' file. Replace the default commercial a/c with similar ones (weight and speed) from your ai aircraft. ( AI Boeing and Airbus to replace Boeings, and I find the CDAI CRJ-200 works well in place of the Dash 8.)

Read the TTools help file for specifics.

Dave

If you normally fly between only a few airports, you can add flightplans for GA or any other aircraft manually to your "FlightPlans.txt" file using MS Notepad.  Just copy an entry for an aircraft with roughly similar flight characteristics and change the times, destinations, and callsigns.  I've added a CAF Rescue Twin Otter in AI traffic to most Canadian airports in this manner, among a few others. Once again, this option can be considered when you normally run between only a few airports, and it doesn't matter to you what's going on AI-wise in other parts of the world. 

For the record, before mention was made here of the PAI default traffic un-installer, I went about it the hard way and manually took out every flightplan associated with the default 737, 747, 777 and MD-80; it took over a month at a few hours each evening to complete .   So unless you have lots of time on your hands, not recommended.