Because the ground slopes!
Runway location is a compromise between geographic location (towns, transport links), suitable ground for construction (i.e. not a swamp, preferably!), relatively level ground (level being ideal) and alignment with prevailing winds.
Since it's unlikely all of these can be met perfectly, some compromise must be accepted.
It is not practical to level the ground in most cases. A 10,000ft runway, 150ft wide and with a 2% slope (typical maximum catered for in perf manuals) would require some 4,500,000 cubic metres of infill simply to bring it level, resulting in a 200ft cliff at the end of the runway. To achieve a safe gradient around this runway-embankment would double or triple the amount of earth to be moved.