The controller wouldn't say "direct as filed." This would be a complete contradiction. I think from looking at the original post, he was cleared direct Boise. I believe that this would mean direct the NAVAID. Generally you are cleared to the navaid or IAF serving an approach at the field so that if you go IMC and lost comm, you can commence the approach at your clearance limit IAW lost comm procedures. Direct the airport would be of no use to you or ATC in such a situation. I found this in the PCG:
DIRECT- Straight line flight between two navigational aids, fixes, points, or any combination thereof. When used by pilots in describing off-airway routes, points defining direct route segments become compulsory reporting points unless the aircraft is under radar contact.
This is pretty vague, but I would think that they are looking for navaids or route structure, etc, not geograpic points such as airports or visual landmarks. Also, I think they would clear you direct "Boise airport" if that is where they want you to go.
Here's an example out of the FAA ATC Order:
Cessna 21A has been cleared to the Airville Airport via V41 Delta VOR V174 Alfa VOR, direct Airville Airport, maintain 9000.
Note the "direct Airville Airport" wording. In looking through the pubs, I can't find anything really black and white, but in all the sections about direct routing, only fixes and navaids are discusses. There's nothing about airports, etc. All the pubs are available on the FAA website, which is really nice, esp for looking at the ATC pubs. The address for the atc pubs is below.
http://www.faa.gov/ATpubs/