The issue is that Chrome actually performs NO checking of any files for viruses. It simply assumes that any potentially executable file is infected. Only after enough people download the file without reporting a problem do they then stop issuing false warnings.
All Google needs to do is revise the language of their warning to be accurate and the problem goes away. Simply tell users the file is unknown and has no history, so the user should be cautious and run some sort of anti-virus scan to check the file before using it. But accuracy like that would apparently be wrong for Google, since it doesn't feed into our alarmist society.
<sigh>