Brian, I've never used Rufus before but I've looked at the executable that is downloadable from their site (the first one, rufus-4.15.exe) and I assure you that it is not malicious. It's possible that Windows Defender is throwing some kind of false positive (although simply running the executable did not produce any alerts here) but I'd need more precise information, in order to determine what exactly is happening.
Could you please document the exact steps one needs to perform, in order to reproduce your results? Which executable did you download? When did the alert pop up? What parameters did you select?
The thing's UI is awful, BTW - apparently you have to click on what looks like a dropdown listbox, in order to open a file selection menu, WTF.