I used to use my mat markings to cut, because I didn't get why it shouldn't work (even though Harriet Hargrave insisted it wouldn't). Then I made a tree skirt using templates, and I was amazed -- all my pieces were exactly the same size and it was so easy sewing them together. So now I use only my ruler to cut, and I find it so much easier and more accurate.
The problem with using the mat lines isn't the accuracy of the mat. It's the difficulty in factoring in the lines themselves when you cut. If I would cut my first piece by positioning my ruler on the outside of a line, and then position it on the same place on the line 2" away (for example), that second cut wasn't quite 2".
I don't know if that makes any sense, but cutting is so much easier and more accurate for me, now that I am liberated from the mat lines!