Haven't read Jefferson or Madison much, have you?
You will have to explain to me how Jefferson and Madison were being religion-neutral when they pushed a bill in Virginia to punish those who broke the Christian Sabbath. Oh, and they pushed for this bill on the same day they pushed for the bill establishing religious freedom, btw.
This was before they got to the national level and before the First Amendment, but it in no way supports your contention they believed in govt. being religiously-neutral.
Also, Jefferson wrote in numerous letters that he believed the right to more forcefully indoctrinate citizens into a religion was the right of individual states.
And, according to the Annals of Congress, available online, Madison explained the meaning of the First Amendment when he introduced it to only prohibit a nationally established, forced religion.
Again, not exactly going so far as to demand religious neutrality.
In fact, during the debate on the First Amendment, Congress specifically rejected amendment changes that would have specifically demanded neutrality on religion.
Those objecting to it during the debates said they thought it went too far, and that view carried the day.
They opposed the idea of a nationally established Church. Many states had established churches at the time of our country's founding.
Check out this link from Answers.com. At the bottom of the page is the list of established American state churches and the time of their disestablishment.