I use the lines on my mat all the time. One, it double checks my math. I can make a mistake counting 3 inches on the ruler, but I know if I started on 0 on my mat, the ruler should always be lining up with a multiple of 3. It has saved me many a time before making a mistake (measure twice, cut once!)
The 2nd reason has been mentioned before- squaring up a piece before making the cut for my project. I can see that the grain is running lengthwise on my mat, and it helps me to trim up the edge to square it up so my folded fabric isn't wonky after the cut when I unfold it.