I would suggest you get the most current maps of the area and figure out what altitude to fly at based on the map information.
Exactly. In real life, no matter what kind of plane or flight it is, the PIC is responsible for knowing what obstacles exist along the proposed route. For casual flying in FS, it only takes a quick look at the map to get a rough idea, and planning a flight in the sim, as stated earlier, will calculate a safe enroute eltitude that takes into account the highest terrain.
This thread suddenly reminds me of an interesting download that does away with the "false moonlight" of the default sim; I tried it for a while before having to re-install FS9, and found it very realistic: that is, at night in the sim with no moon, you can't see a damn thing except stars (if it's clear) and lights on the ground. Nothing. When using that add-on, it's important to make sure your destination airport has lights (not all of them do).

It's lousy for night screenshots, too.... but if you're after realism, it's critical. I have very few real night hours logged in RL, but I can vouch for the fact that when you take off from a rural airport on an overcast night, once you clear the runway lights and start climbing out over woods, you are flying pretty much by instruments, until you level off and can use a highway or town's lights to reference your horizon. It's challenging.
Can't remember the name of the file, unfortunately... if anyone's interested I think I still have it stashed somewhere at home; been meaning to re-install that in the sim anyway.
What would be ideal for realistic night-flying in FS would be not only properly dark sky and clouds, but surface-light reflection on cloud bases- ideal for those night flights when you're not 100% sure if that city is dead ahead where it should be...