Hi phillmckraken,
I just downloaded both the win and win32 MewnBase builds from the game's itch.io page, and scanned them both with Windows Defender on multiple Windows machines, each with updated virus definitions, and nothing was flagged as having malware.
Try using the Itch Desktop App and downloading the game through there and see if it still gets flagged for you?
If anyone else with a Windows machine could give the zip files a scan and let me know if they come up clean or infected, would be greatly appreciated.