Is it normal that most or all rooting apps get so many virus warnings? For example, here are some results from VirusTotal:


TowelRoot
The variants of Framaroot (1, 2, 3)


Why is that? Can anyone point to a clean rooting app?
Yes, it's normal. Think about what a rooting app does. It exploits a vulnerability in the operating system to get elevated privileges, and drops a new binary so that it will continue to have those privileges, completely subverting the security of the system. In a way, a rooting app is a virus. You certainly wouldn't want to install one by accident, so it's correct that your antivirus should warn about it.

If you want a "clean" method of rooting, the only way is to use the official method, by unlocking your bootloader and using the recovery to root.