As a simple pax I can see a problem with armed pilots - from the terrorist point of view the pilot is a known threat - i.e. he/she knows where they sit and, (I'm guessing here), through the freedom of information in America, would probably know what weapon they were carrying. Based on that information they could probably work out a time when the pilots would be at their most vulnerable and attack then.
Air Marshalls on the other hand are an unkown quantity to the terrorist - are they on-board, is there more than one, where are they sitting or are they pretending to be crew, etc.? In my mind a much more effective way of dealing with the issue. It would also re-assure me that the pilots are keeping to their day job, and the Marshall to theirs. Seems to work for El-Al anyway.
The other thing that comes to mind is that the pilots in America are not the only ones allowed to carry weapons. There was a post to that effect in January 2003, in
this thread which listed the other people in the list. I'll reproduce part of TR4A's post for your convenience.
The following Federal agencies may be armed during flight -whether on official business or not.
-Bureau of Printing and Engraving
-Coast Guard
-Customs
-Defense Nuclear Agency
-Dept of Agriculture (Poultry Inspectors, etc)
-Dept of Commerce
-Dept of Education
-Dept of Health and Human Services
-Dept of Labor
-Dept of State
-Dept of the Air Force/Army/Navy
-Dept of the Interior
-FBI
-General Services Administration
-Postal Service
-Secret Service
-Bureau of Alcohol, Tobacco and Firearms
-FAA
-IRS
-Dept of Transportation
-CIA
-DOD
-Dept of Energy
-Dept of Housing and Urban Development
-Dept of State
-Dept of the Treasury
-National Security Agency
-DEA
-Federal Prison System
-Federal Protective Service
-Marshals Service
-Smithsonian Institution
All you need is for someone to forget to tell the Cap'ain that someone from that list is on board and..
I think I'll take the train, thanks