If someone says they are [insert belief here], then we tend to take them at face value. To do otherwise would be to start down a long and slippery slope of passing judgements on historical figures, something that is diametrically opposed to the practice of good history. If someone acts significantly outside of orthodox belief structures, we might say that a person "considered himself/herself to be Christian" as a way of marking their heterodoxy, but not as a refutation of their own claim of faith. After all, for historical study, what a person thought of themselves and what others thought of them is precisely the point, not how they measured up to an abstract set of criteria particular to a specific subset of the population.

There were and are many, many Christian sects that do not consider others who consider themselves to be Christian to be so. That the latter group considers themselves such, and that the former does not is the relevant subject for historical study.

Historians do, though they frequently qualify that by setting aside a number of the founding fathers as Deists, which is a now-defunct subset of Christianity.

That said, there's a number of former presidents that, if imported into the modern day, would almost certainly be vilified by Christian fundamentalists and those on the religious right as unchristian or irreligious. I can't imagine a 21st century national political figure, much less a president, getting away with an experiment like the Jefferson Bible or making statements about organized religion in the way that Ben Franklin did. Yet both of them professed to believe in a Christian god, and historians have no clear or overwhelming evidence to suggest that they were being disingenuous about that.

James Monroe left no evidence to suggest he adhered to any particular religious faith, but no evidence to suggest otherwise, either. Andrew Johnson professed faith and sporadically attended church with his wife, but wasn't a member of any church and didn't seem to be particularly attached to any particular sect. Rutherford B. Hayes and others fall into a similar category of figures that had faith in a Christian god, but weren't particularly observant or devout.

Moving into a more 20th century framework, there's also Nixon (who was a Quaker - an obviously Christian sect, but one that doesn't adhere to a lot of traditional aspects of organized Christian religion).

The reason that the debate exists isn't that there's convincing historical evidence to suggest that any one of these figures identified as atheist or belonging to a non-Christian religion. It's because there's debate about what it means to be a Christian, and the way that many of these men lived their lives as people who believed themselves to be Christians falls short of the mark that some Christians feel need to be met in order to qualify as such.