The notification does not say your project has malware. It is only a warning that you account was recently created and uploaded something. Once you establish reputation in our system then these types of warning will no longer appear. Some pages are subject to human review and may show a warning until then.
More information about our indexing process here: https://itch.io/docs/creators/getting-indexed#why-isnt-my-project-showing-up
Hope that helps