Hmm that's a bit odd. When you run the exe it should automatically unpack 4 programs to the folder location of where N64Rip.exe is:
Then after doing that the Frontend itself should start running and you'll get this:
To clarify, N64Rip.exe IS N64Rip.exe, all of the code is in the exe you can download by itself or in the zip version. It won't extract another copy of itself. I do however agree with the antivirus thing. Some antivirus programs are really stupid and see any program packed in UPX (which mine is) as a virus. I'll go upload an normal non-packed version and see if that helps. Note it will be twice as large.
If you want to try using the offical links, as I've only JUST updated the tool on this site:
N64Rip.exe not upx compressed
The only difference between the zip version and the exe version is that the zip has a readme.txt file and the exe. If you were really having trouble extracting the exe from the zip file just go for the exe download.