Historically I've always uploaded my website via FTP since my server does not have front page extensions and nor will it.
Using the latest release of Visual Studio 2012 (11.0.51106.01 Update 1) (although I think this issue is for all of 2012), I cannot publish my website!
The error message is
2>Unable to add 'file' to the Web site. FTP Passive mode is not available
I will also point out that my connection validates so I don't think the error message is anything but clear and meaningful!
So, I have 3 questions.
Open your publish profile Properties\PublishProfiles\your_profile_name.pubxml
Add <FtpPassiveMode>False</FtpPassiveMode>
to <PropertyGroup>
Save file and publish again.