Great advice given above, and all I'll add is make sure you are working on a surface that is the correct height for you so that you can both see your work and get even pressure on your ruler as you cut.
I routinely cut 4 to 6 layers, sometimes up to 10 or 12, and my cuts are almost always right on. But it is a skill, and as with all skills, you have to use good form and practice.
RST