wyUpdate is not listed as a virus by any major virus scanner. See: https://www.virustotal.com/en/file/aa71c676499260ed07b6b0e54aff155ad8e46b49aee933e90b5ff4dd098aadb6/analysis/1441380325/
Make sure you're using our build of wyUpdate. It's signed by us. Don't use custom versions of wyUpdate unless you know how to ensure that there are no false positives. Also, some virus scanners / "system protectors" incorrectly flag files that are run from the %appdata% folder. So, make sure your app is installed in Program Files.