Most commercial flights are between 29,000 and 42,000 feet in altitude apparently. But I realise I don't know why. My guesses are:
Actually most jets (commercial and private/corporate) fly at high altitudes (generally as you describe in your question) because the lower air pressure (thinner air) results in less drag on the airplane. Consequently, this results in better fuel efficiency and a faster speed through the air.
Flying at a lower altitude (over the ocean or any place else) would reduce the substantial benefits (fuel economy and speed) of flying at a higher altitude.
Optimum cruising altitude is a delicate balance between air density, lift, drag, and engine performance.
Thinner air at high altitudes means less drag, but also less lift and less power.
Today’s modern jetliners are optimized for about 35,000-40,000 feet for the best speed and fuel efficiency. Weather and wind direction can sometimes cause lower altitudes to be more efficient.
As usual in the aerospace world, it is a matter of compromises. First the pros of flying high and then the cons.
Commercial jetliners follow a flying path which resembles a stairs where the flying altitude is increased in steps till the limit of some 10km.
This increase in altitude is due to the fact that, during its flight, a jetliner diminishes its weight due to fuel's consumption. In order to compensate for the lower and lower weight, lift must be reduced accordingly and that can be achieved either decreasing the AoA (i.e. $C_l$) or decreasing the air density $\rho$:
$L=½ \rho V² S C_l$
Decreasing $\rho$ is easy since you just need to fly higher. Changing AoA would also be easy to obtain but the aerodynamic shape of a jetliner is optimised to be very efficient within a very narrow range of AoA; plus, try to push a cart along the aisle with a -5° attitude :)
Another positive effect of flying high is that, obeying the drag a very similar equation like the one of the lift, less air density implies less drag as well.
Flying high would appear so far to be a good thing, so why not flying higher?.
At higher altitudes engine's thrust reduces as well: said 1 the thrust generated by a modern turbofan as measured on the testbench, at 10km height and Mach 0.8 that thrust can be as less than 0.3. And here we hit a first limitation: going higher and higher thrust decreases more and more but faster than the decrease in drag and at a certain height there's simply no thrust left to counteract drag or to manoeuvre the aircraft. This height is called ceiling and for example for an A320 is some 12.5km. Obviously if there is a need to fly higher (Concorde for example), thrust can be increased but at the expense of a higher fuel consumption $\Rightarrow$ more fuel $\Rightarrow$ more weight.
Another limitation of flying higher is structural: the cabin has to be pressurised to a value which is comfortable and let the passengers freely breathe. So the fuselage is basically a tank and the weight of its structure is proportional to the pressurisation level. Flying higher would imply the need of a higher pressurisation and therefore a heavier fuselage with all that implies: more weight $\Rightarrow$ more lift $\Rightarrow$ more drag $\Rightarrow$ more thrust $\Rightarrow$ more fuel consumption $\Rightarrow$ more fuel $\Rightarrow$ more weight.
A third limitation is that in case of a sudden depressurisation, if the altitude were too high, passengers wouldn't even have the time to put the oxygen mask on their faces. That's the main reason why the Concorde had so small windows and a very powerful pressurisation system.
Another limitation is due to stall speed. We rewrite the previously written lift equation in $V$:
$V=\sqrt{\frac{L}{½ \rho S C_l}}$
Now, $L$ equals weight $W$ and $C_l$ is limited by its maximum value $C_{l_{max}}$ before stall (which is more or less 1.3 for a jetliner without flaps deployed). Substituting these values we get the minimum speed at which the airplane can still fly before stalling:
$V_{min}=\sqrt{\frac{W}{½ \rho S C_{l_{max}}}}$
As it can be seen, this minimum speed before stall increases at higher altitude due to the decrease in $\rho$. Flying higher would therefore imply the need of flying faster to stay well away from the stall condition. Obviously to fly faster an airplane needs more powerful engines with the same negative implications as before.
I cross the USA a lot in an automobile and I watch my MPG. Guess what happens to my MPG when I'm in high-altitude Utah-Wyoming.
Drag (which causes fuel consumption) has two components.
This is the additional "drag" created by using the wings to create lift to carry the weight of the plane. The induced drag is proportional to vehicle weight.
My car does not have induced drag because it sits on wheels. I do have some rolling resistance that is proportional to weight (because of the way rubber tires work), but trains don't (to speak of; it's inconsequential by comparison to any other mode).
This induced drag is not significantly affected by altitude.
This is exactly the same aerodynamic drag that airframe shape would have if its weight was fully supported by railroad wheels. Simply pushing that shape through the air at 600 mph takes a lot of energy.
This is very affected by altitude - like with my car getting better MPG at high altitudes. Same with an airplane - the higher you fly the better your "MPG" as it were.
So induced drag is a wash, but parasitic drag improves as you climb.
