Most likely you are not doing it correctly. It does take a while to figure out the best way to use it. Once you get to know what it’s doing then it’s not that bad. If you just keep flattening the same area that is mostly flat but inclined over and over it really doesn’t do much. If you want to flatten an area, find a small area that is 2x2 or 2x3 that is flat or really close. Flatten it once to get it flat for a building. Then take that 2x2 area and expand it to a 2x3 area. The flatten tool averages the land. It may take a couple passes, but they are short. Once you have a 2x3 area then you are golden. Now the 6 squares you have will pull any 2 slightly lower/higher squares to their level. If the 2 are a bit different then you may need to do the 2x2 again, the 2x3 again, then the 2x4 to get it flat. But this is generally only when the land is really steep. Just keep expanding that area out one row at a time. If the change is large enough to affect your reference area, then you have to redo the smaller area sometimes.
Eventually you can do things like this:
