They are not rebranding Go Transit, they are rebranding Metrolinx (which, besides Go Transit, includes UP Express, the PRESTO Card and joint procurement for municipalities). The fact that you have confused the two makes it clear why the rebranding is necessary. Most people I speak to on a regular basis (people who don't read UrbanToronto) do not know the difference either.
I personally do not think this re-branding is very effective in addressing the issue, and I even concede that there is an outside chance that some backroom dealing is possible here (as I know nothing about how the re-branding was accomplished). But I think it's hard to argue that Metrolinx does not need to raise public awareness of what it does.