I have soil with a lot of clay in it and few stones, so it's not too hard to get level. I've got flagstone in a couple of small areas. Some of it is on a bed of gravel and some of it is on bare soil. I don't see that one is any worse off than the other. I was just curious if the sand/gravel bed typically installed under flagstone is for drainage, ease of leveling, weed control, pest control or other..
Leveling, drainage, and protection of the flagstone, especially in freezing climates. Basically, in heavy soils, water can pool up under the flagstones and produce frost heaves, which will allow the flagstones to break much more easily. The sand and gravel produces an even base that supports the whole stone, and keeps it from cracking.