He didn't note that Madison (and Thomas Jefferson) opposed presidential proclamations calling for prayer or other religious exercises. Madison's view is worth reading in full, with special emphasis on this sentence:
The last & not the least objection is the liability of the practice to a subserviency to political views; to the scandal of religion, as well as the increase of party animosities. Candid or incautious politicians will not always disown such views. In truth it is difficult to frame such a religious proclamation generally suggested by a political state of things, without referring to them in terms having some bearing on party questions.
Short version: Unscrupulous talk-show hosts like Sean Hannity can easily turn prayer proclamations into opportunities for short-term political gain.
Dobson, I am sure, would have a hard time understanding why someone like Madison could think religion is important but also think that it should have nothing to do with government. But the founders understand that keeping religion separate from politics would strengthen, not weaken, religion. That was still obvious to de Tocqueville when he visited America decades later and attributed the powerful influence of religion in American life to its divorce from the political world. He wrote, "Hence any alliance with any political power whatsoever is bound to be burdensome for religion. It does not need their support in order to live, and in serving them it may die."
Somewhere around the early 1950s, though, the message seemed to get lost. That's when the National Day of Prayer was created and when "Under God" was inserted into the Pledge of Allegiance. With the threat of godless communism looming, we lost our nerve, and some of us still haven't gotten it back.