In 1950 a car cost ~$1.5K in the US, GDP per capita was ~9.6K. So it was around 0.16 of GDP per Capita to purchase a new car.
In 2016 GDP per capita had risen to $53k with a new car costing between 17K and 33K depending on how you look at it. This is 0.32 to 0.62 of GDP. More, but not horrible.
A Cessna costs $160K, a 3x factor compared to GDP. So for around the price of a house (or down-payment) you can own a depreciating mechanical liability that enables you to commute marginally faster...
The economics aren't there.
For what it's worth, I don't really see personal aviation take off anytime soon anywhere near as much as personal driving has - but some niches might become feasible with personal electronic VTOL aircraft (PEVA).
And anyway, even if it cost that much, it's still a viable route for commuting using a rideshare service like Uber if you have 3-4 people sharing the same vehicle and you're shaving off 2 hours of commuting each day (500 hours extra per year at $30/hour gives you $15,000 extra per year PER PERSON).
I imagine the same applies to air commute, considering most people will be converging into a small number of waypoints.
a) you don't have to stick to airways. They're largely for ease of planning and navigation with ground-based navigation aids (NDBs, VORs). You can easily fly off airways, and (in general aviation planes during visual flight) nearly always do.
b) with the advent of GPS, "direct" flight routes (not involving airways) are becoming increasingly common.
c) The "big sky" is not a fallacy. Think about it: first, on the ground you can only drive where there are streets. In the sky, you can fly everywhere (even on a 2-D plane), plus then you have the third dimension. There is plenty of space, and congestion won't be a problem unless regulatory/technical issues impose bottlenecks. Airports are natural bottlenecks, but what is envisioned here are VTOL aircraft, so the number of suitable take off and landing places would multiply.
d) The "navigation paradox" [1] is that improved precision in navigation leads to increased risk of collision, because where in the past airplanes where only approximately on an airway (and would most likely miss each other in case of ATC mistake), now they're precisely on the airway (and will collide in case of ATC mistake), see the case of the GOL and Embraer in Brazil [2]. However, that is a shortcoming of current ATC practices, not inherent in flying.
e) I don't understand your point regarding property law. You can hop on a Cessna at Palo Alto or San Carlos airport and fly over the Golden Gate Bridge, San Francisco, Oracle, Stanford, SLAC, San Jose, with no problem. The airspace is there and it's open.
Bottom line: with modern navigation methods, air space congestion will only become a problem after personal aircraft have become tremendously popular and prevalent, if at all.
[1] https://en.m.wikipedia.org/wiki/Navigation_paradox
[2] https://en.m.wikipedia.org/wiki/Gol_Transportes_A%C3%A9reos_...
For reference, a Cessna 172 flies around 110 knots = 125 miles per hour, and uses about 10 gallons per hour, so it gets about 12 mpg.
Granted, that's pretty bad, but that's about 1950's technology, and it's not orders of magnitudes.
And in 3D you have MUCH more space (in fact, one reason that there are so relatively few mid air collisions is just the fact that "the sky is big".)
So, I don't think aviation is out a priori "because physics".