I really like to use a Gingher ruler and a Gingher or Fiskars mat. The lines are thinner and I think it is easier to get accuracy. If you can't do that, try lining up your fabric at the line, place your ruler where you want to cut. Then before cutting, get a small ruler (I use the one with the slidey thing in it) and check the measurement from the edge of the fabric to the edge of the placed ruler. If that jives with what you are after, then make sure when you cut that you hold the rotary cutter in a straight up and down position relative to the edge of the ruler.
Another trick -- after you have your ruler placed is to see if the quarter inch and eighth inch marks on your ruler match up at the top of the mat and at the bottom of the mat. These lines are usually thinner on the ruler and on the mat and can help in accurate placement.
Again, as others have said, whatever method you use, be consistant.