As Tom said, make sure the filed altitude is what you want but it will default to ones which meet the requirements for the route segment to be flown.
In general terms there is a requirement to be at least 1000 ft above terrain/obstacles on the intended flight path.
However, on Airways and other controlled airspace there is also the issue of Minimum Enroute Altitudes which are determined by signal reception (VORs and NDBs) that make up the airway and define airspace and Minimum Obstacle Clearance Altitudes. VOR signals particularly, being line-of-sight, would be blocked by terrain at lower altitudes in the middle of a long leg (or even the curvature of the earth) requiring the MEA to be high at some point and ATC is bound by these when issuing clearances.
§91.177 Minimum altitudes for IFR operations. http://www.ecfr.gov/cgi-bin/text-id...ext&node=14:2.0.1.3.10&idno=14#se14.2.91_1119
On a VFR plan the pilot is expected to maintain such altitudes but you won't get vectors etc. On an IFR plan the onus is also on ATC to ensure the requirements are met or a clearance normally won't be issued. Bear in mind that FS airspace and rules are less-precisely defined, mapped and controlled (it is only a $40 program after all) than in the real world so the rules and airspace are more generic. The built-in ATC rules are fairly rudimentary but give some degree of reality.
As far as cabin altitude is concerned, pressurization is not required but supplemental oxygen is under conditions. In the US they state:
[h=2]
§91.211 Supplemental oxygen.[/h](a)
General. No person may operate a civil aircraft of U.S. registry—
(1) At cabin pressure altitudes above 12,500 feet (MSL) up to and including 14,000 feet (MSL) unless the required minimum flight crew is provided with and uses supplemental oxygen for that part of the flight at those altitudes that is of more than 30 minutes duration;
(2) At cabin pressure altitudes above 14,000 feet (MSL) unless the required minimum flight crew is provided with and uses supplemental oxygen during the entire flight time at those altitudes; and
(3) At cabin pressure altitudes above 15,000 feet (MSL) unless each occupant of the aircraft is provided with supplemental oxygen.
In Canada:
1. All crew members and 10 per cent of passengers and, in any case, no less than one passenger --Entire period of flight exceeding 30 minutes at cabin-pressure-altitudes above 10,000 feet ASL but not exceeding 13,000 feet ASL
2. All persons on board the aircraft -- (
a) Entire period of flight at-cabin-pressure altitudes above 13,000 feet ASL
Regulations vary in other jurisdictions.
So, to go above 10/12.5/14 K ft you only need a supplementary oxygen supply and that's not generally modeled so you can pretend it's installed. Now, it may also depend on whether your aircraft can get that high, but that's part of flight planning. However, if you can't comply, ATC can't issue an IFR clearance.
Pressurization only reduces the 'cabin pressure altitude' to below the above limits to preclude oxygen use but at the cost of building a pressurized aircraft structure.
