> Is there something more subtle going on?
Yup.

Before I get to what that is, here's the real problem: you have to contact ATC to file an instrument flight plan. If you're flying visually, interaction with ATC is limited to communications with the airport's tower, maybe with one of the major ATC centers if you're departing an airport with designated approach/departure frequencies (i.e. a Class B or C airport).

Visual flight (VFR) into instrument meteorological condition (IMC) accidents are fatal somewhere between 75% [1] and 90% [2] of the time. For the reason over the last two decades barriers to instrument training have been steadily decreased: used to be you had to have 200 hours in the book before you could get an instrument rating. That was decreased to 125 in 1986 and in 1997 the flight time requirement was dropped altogether [3].

The reason for this is that flying instrument flight plans have a lower accident rate [3] than pilots flying VFR. Furthermore, pilots on a VFR flight plan who run into IMC and are instrument rated can contact ATC and file a pop-up IFR flight plan, interacting with ATC to establish vectors around convective areas (thunderstorms) and into an instrument approach.

Accident rates increase when barriers to instrument flight are erected. A good example of this is when the Commemorative Air Force barred pilots from filing IFR flight plans. They reversed this policy after irreplaceable historical artifacts were lost due to pilots trying to dodge under weather to make an airshow or get home.

Now, to the examination of the WH's communication on the matter and to your question of whether something more subtle is going on: https://wwws.whitehouse.gov/petitions/!/response/why-we-need...

The example in the letter of the "large commercial aircraft" vs a "corporate jet" is invalid: the administration is conflating the excise taxes that a FAR Part 135 commercial operation pays per passenger vs the fuel taxes per gallon that a FAR Part 121 corporate flight pays.

The "something more subtle going on" is revealed in the language of the letter. This is going to lead into my sharing a political perspective, which I know is verboten on HN but is not avoidable in the context of this little digression.

They exempt piston flight, military, emergency, etc. And they single out a corporate jet as an example of a flight not paying its "fair share" for use of ATC resources. It's a not-terribly-subtle attack on corporate aviation.

I could defend the validity of corporate aviation, but I won't at this juncture: the problem is that their attack is poorly targeted and will have considerable collateral damage. For example, there are hundreds of small air-taxi operations that operate out of FBOs around the country, like the one from Addison, LA to Shreveport, LA that does four flights a day every day of the month. That's an additional $200 a flight x 4 x 30 for an additional $24,000 that the operation is going to have to come up with. Given the thin margins these operations run on, these user fees place the jobs of the pilots, mechanics, and FBO personnel at risk.

Furthermore the WH is pretending that Air Traffic Control is the only thing that the FAA funds in order to justify their claim that it isn't fair that a Southwest 737 pays more taxes than Apple's Gulfstream V. But the taxes that the FAA collects go toward airport maintenance grants, maintenance of the aging VOR-VORTAC system. Generally, support of the air transportation grid. The ATC is just one significant facet, but not the only facet.

As to your question about the ATC unions, they don't have a voice as the WH can (and likely will) assert these user fees via Executive Order.

[1] http://www.humanfactors.illinois.edu/Reports&PapersPDFs/...
[2] http://www.aopa.org/asf/hotspot/vfrimc.html
[3] http://www.shashek.com/Flight_Logs/Docs/iPilot_Articles/Shou...