Concerning the American Indians, by the Spring of 1648 most of them had died as the Old World diseases overtook them. Later on Mountain Men and other explorers would spread these diseases to the few inhabitants who had not yet been exposed. I think it was Lewis and Clark who nailed the Mandan (among others).
My sources inform me that the first French colony (1540-1543) was initiated by Jean-François de La Rocque sieur de Roberval, who becomes the general-lieutenant of Canada.
Roberval was a Huguenot. You may be correct about the captain of the fleet, Jacques-Cartier, being a Catholic, although probably not a very good one. Roberval's commission give him the right to construct , forts, churches and temples. It is supposed that both religions can have their institutions.
I am personally much more interested in Chapigny, a Protestant who married "up", who became later in life the Intendant of Canada, and his close relative, Cardinal Richelieu. Now these guys are "fun" FUR SHUR. Roberval and Cartier probably got along equally famously.
According to many sources the Huguenot "headquarters" for their portion of the North American fur trade was along the Green River in Western Kentucky (a territory first reported on by DeSoto). They tended to stay South of the French Catholic areas, although I find records suggesting many of them were careful to attend mass in Roman mission areas such as Vincinnes. It's probably a case of protective coloration eh. Still, the Iriquois Indians traveled from New York to Beauval Saskatchewan, a two year round trip, to collect furs. They traveled with Huguenots.