I've been kind of curious about the whole "America began as a Christian nation therefore it must now be considered a Christian nation and it is proper to acknowledge and support Christian dominance in society and government to exclusion and detriment of secular and non-Christian beliefs" concept. I should probably disclose that I see some possible flaws in the reasoning even if the beginning-as-Christian is true. But what about the whole assertion without providing evidence that American was founded as a Christian nation?
Unfortunately, the extremely long NY Times Magazine article on this, won't tell you much. It bumbles around in Texas school textbooks politics and general politics before getting to a wishy-washy claim, also without much evidence, that America was less religious than the Christian fundamentalists claim but more driven by religion than textbooks acknowledge. The thousands of words never even got around to discussing Christianity's negative and positive effects on slavery, treatment of Native Americans and women, and on foreign policy.
Worst of all, the article failed to provide a metric to use in analyzing how Christian was America in the 18th Century. I can give two possibilities: what percent of Americans were Christian back then, or what (subjectively defined) ratio of the intellectual firepower behind America's founding was from Christians. It's also necessary to define Christian. Fundamentalists are pretty clear on what that means today: a set of beliefs about Jesus Christ as the only son of God born of a virgin and killed by men, who rose from the dead after the third day, and whom each Christian must personally accept as his or her Savior. The fundies get a little fuzzy in applying this definition to 18th Century Americans, but let's be consistent.
As to what percent of the population was Christian, I don't know, but I'm sure it's far less than the nearly everyone, as fundamentalists seem to think is the case. I would guess over 50% were Christian but not more than 90%, maybe much less. You have three significant groups to consider: first, Native Americans east of the Mississippi. There were still a lot of them in 1776 and many/most weren't Christian. Second, African and African-American slaves, many of whom were forcibly brought from non-Christian Africa or were the first generation born in the New World, and many weren't Christian as the fundamentalists would define them. I'd guess nearly none of the slaves brought from Africa were Christian, and half of their children weren't either. Slaves formed a declining percentage of US population over time. In 1790 they were just less than 20% of the population, so they would have been more in 1776. What's unclear is how many were the first or second generation from Africa, although over 600,000 slaves total were brought to North America, mostly in the 18th Century.
The third group would be Jews and other whites who failed to personally accept all tenets of fundamentalist Christianity. I think saying 5% of all whites fell in this category would be a low estimate. The three groups together has to be over 10% of the population, maybe much more.
The other metric, looking at the specific Founding Fathers, is a lot trickier. While all of them were influenced by and generally accepted philosophies that had Christian origins, the ones who could qualify for membership in a fudamentalist Christian church would be a much smaller percent.
It would be interesting for someone to put some time into measuring either of these metrics - say, the time that the NY Times put into writing its article. I think its clear though that the percent that were Christian by either metric doesn't approach, say, the percent of climatologists constituting a consensus on climate change. A large non-Christian component of American society was there from the beginning, and deserves its own place in society.