Because this is a user-specific file, it should be excluded from version control. From https://msdn.microsoft.com/en-us/library/ff398069(v=vs.110).aspx, emphasis mine.
When you create a publish profile, two files are created in the PublishProfiles folder: .pubxml and .pubxml.user. The .pubxml.user file contains only a few settings that apply to a specific user, such as an encrypted password. By default it is not included in source control. Typically when you change settings related to a profile you edit the .pubxml file rather than the .pubxml.user file.