1) American civilization began with Jamestown and Plymouth Rock--i.e., when white Anglo-Saxon Protestants came from England to settle the Atlantic coast. FDR didn't think the Spanish who explored and colonized the South, or the French who explored and colonized the Great Lakes area. And of course he didn't think about the millions of Native people who'd been here for 10,000 years or more. To him, American civilization = British civilization.
2) What exactly was the previous danger faced by the English colonizers? Who weren't Americans, by the way, and wouldn't be for another 169 years. The harsh climate? Maybe, although calling that a "danger" is a stretch. The colonizers could've rectified any setbacks caused by cold winters and failed crops with more people and supplies. These problems were technical in nature and spending enough time and money would've resolved them. (Which is what did happen, in fact, as more and more ships arrived.)
No, the real danger these colonies faced were the "savage" Indians. You know, the people who owned and occupied the land the foreigners wanted to appropriate. The people who welcomed the strangers and kept them alive until they realized the strangers were planning to take over their fields and streams.
The implication is pretty clear. Hitler was the greatest threat to Euro-Americans since the "merciless Indian savages." The Nazis were the barbarians of the 20th century and FDR wanted us to be equally resolute against their evil.
Alternate version of the speech
Here's what FDR could've said instead. What a Native leader might've said in his place:
Below: Three milestones of Western imperialism.