First off, you need to understand that this isn't just you. It happens to all kinds of projects.
That's Git several hours after release. Symatec thinks it's not trust worthy too. Bmarguiles is absolutely right that the "easy" way to deal with this is to have a large number of users. Then, this will magically take care of itself as the AV vendors see more instances of the software.
That's not very practical for a young project though. That warning is scaring off the very same users you need to make that warning go away. The solution here is to start blanketing as many AV vendors as possible with Whitelist requests. Each vendor has a different process, but it generally involves filling out a form, attaching your installer, and sending them the request. Wikipedia has a non-exhaustive list of notable AV software that would be a great place to get started. Settle in though, because it's a big list and you generally need to do this every time you release. At least until you have a good reputation with a consistent user base. Honestly, as often as we release our project, we just don't bother making whitelist requests, but it could be manageable if you're only releasing a few times a year.