This was brought home in episode seven of season 4, when Toby Ziegler (The White House Communications Director) told the President that his ex-wife was pregnant. When asked why he had waited so long to tell them, Toby admits it is because he was 'intimidated by his Catholicism. Bartlet's response is so simple- but it really ties the before mentioned theme together. He simply says "Really? Its my Catholicism, it works for me." There it is. The President makes the powerful point that you shouldn't judge others by your religion- you should follow the moral compass you believe in and let others follow their own path.
As simple a message as it is, its one that I feel is still a major problem out in the real world. Most recently has been the huge outcry against letting Gay Scouts in the Boy Scouts. I'm an Eagle Scout, and I know what its like to go out camping and teaching the skills many kids don't get anywhere- survival, sure, but more importantly leadership... and acceptance. I rejoiced when the Scouts repealed their ban (at least partially) because I believe that know some kids who wouldn't of had the opportunity to be part of the experience before now can. Better yet, they can without having to hide who they really are. What I can't believe is that this is even an issue. If we lived in a world where even most of the people prescribed to concept of following one's own beliefs and keeping the sin of judgement from their lips and minds- this ( and many other religious areas of concern) would be a non-issue.
So, I suggest that everyone evaluate their thoughts and actions, and see if you can live to your own standards of a good, moral, and happy life. You'll be happier if you do- I guarantee it.