My wife went to a meeting last night of religious and secular people to air out their differences with each other. While these meetings may cause personal respect between one group and the next (which is a very good thing unto itself), they are unlikely to cause either group to see things from the other side's perspective.
My wife gave me two examples from the secular side:
1) A former yeshiva boy who stopped being religious in the army was at a shabbos get together with some army buddies. He opened a bottle of wine and asked a religious boy to make kiddush. The religious boy said it was יין נסך, forbidden wine, because it was opened by somene who was not shomer shabbos. He was so put off by that that he decided he didn't want to have anything to do with religious people. (we're not going to discuss the halachic aspect of this case, but there are opinions that say that the wine is forbidden and opinions that say the wine is not forbidden)
2) A couple adopted a child and wanted to convert her. The rabbinical court said they had to sign a paper saying they would send her to religious schools. The couple refused to sign the paper because they didn't want to "lie to themselves and to to religious court." They thought that was such a horrible experience that it left a strong distaste in their mouth for religious people. (They did sign the paper in the end and sent the child to some religious schools.)
On the religious side, the issues that I have heard are more along the lines of:
If they are not going to keep shabbos or kosher then I don't want my children playing with their children because it is much harder to raise your kids religious when their friends from school are out at a movie on Friday night. It is hard to send them to a nonkosher house where you don't know what they might eat. Therefore, we don't want non-religious kids in the religious school.
The issues, as a whole, seem to be that secular Jews want to be able to do anything they would like to without barriers. In other words they do not want religion to be a factor in their life. Religious Jews want to hold onto their code of behavior and are not willing to compromise so as not to offend someone.
An example I gave to my wife is, I don't complain when my co-workers always go to a non-kosher place for lunch on Thursday, even though I am automatically disqualified from going. However, they would be very against a company rule saying that they had to eat at a kosher place, so that I could go too.
In both the situations that the seculars mentioned, there is nothing that could be done from a religious perspective. If you're going to be offended and hate me for the rest of my life if I won't drink something forbidden, there's nothing I can do about that. Hours of explaining are not going to change the fact that if it is only forbidden food because you touched it. The religious guy didn't tell the secular guy, as far as I know, that he was a bad person. He told him he wasn't going to drink the wine. The secular guy in this case was not harmed at all by the first guy not drinking his wine. His pride may have been hurt, but that is because he doesn't understand the law and he doesn't want to understand the law.
In the second situation, the couple was actually hurt. They just wanted to raise a child in Israel. Non-Jewish children are second-class citizens in Israel and the parents wanted to bring the child up as a cultural Jew. However, there are 2 ways to become Jewish. Being born into it and converting. If you're born into it and you don't want to follow the rules, there is nothing we can do about it right now. You live your life and we'll live ours. But if someone else wants to become Jewish, one of the requirements is to accept on yourself Jewish law. They are very lenient about that here, making the couple sign a paper, which they never really have to follow, that they will teach their child what being Jewish means.
This is a battle that is being fought across the spectrum of life. Secular people wanting to live a life without limitations and religious people holding strongly to their values. Groups like this will help explain each side's perspectives in a nonconfrontational manner, but in the end the result is the same.