Secularism is quite different from atheism. I say the pledge but skip the "under God" part, as I don't believe the Founding Fathers intended freedom of religion to imply that one should have to believe in anything.
I was lucky in that my parents taught me to think of the meaning while saying the Pledge. I decided that I would always say it because I agreed with what it stood for, but they would have stood behind me regardless of if I did or did not.
It's my opinion that educated patriotism is much better than blind patriotism, especially in a country like the US. I truly believe that the US is the greatest country in the world, and that is important to me because I got to that conclusion through information and not indoctrination.
Sorry if I'm rambling or seeming to boast.
Tl;dr: If you want to say the Pledge (and you should, ideally, as patriotism is important) you should know what and why, instead of simply going along with the herd.