There are so many things that can cause a late period, not just pregnancy.
It can depend on how old she is: if she is still in her early teens, she might not have established a completely regular cycle. If she is older, she may just have an irregular cycle, meaning that she can have short and long cycles.....even 40 day cycles. Stress can also cause a late cycle.
If you have been on "safe' sex and using it properly there is a slight chance that she may be pregnant, since there is not method that completely ensures that she will definitely 100% not become pregnant.