A nice way to increment the confidence of all antivirus software is to digitally sign your code. Thawte has the cheapest well-recognized certificates starting below 100 € / year.
Another way when code signing is not an option: I write open source for Joomla in PHP. After I received the first indications that Avast marked my file as a (false) positive, I contacted them and they whitelisted my file within hours.
In order to make my life easier, I am creating a separate file with the supposedly “dangerous” function, so that future changes to the program won’t require to resubmit it for whitelisting.
Possibly the speed in their response was helped by the fact that reading a short PHP file is faster than reverse engineering compiled code; nonetheless they were kind, quick and effective.