The first couple of down strokes nothin is stopping the piston from forcing the air out of the crankcase.  On the upstrokes, all we have is atmospheric pressure trying to fill it back up again.  There's a screen in the way too.  So forcing the air out is a piece of cake, while forcing the air back in is a slower process with significantly less pressure to work with.  So in normal operation, more air is forced out than is returned.  So you end up with a very small vacuum.