From the beginning, when people started talking about Secure Boot some warned about the treat to Free Software, but they were pretty much dismissed by many as a bunch of hippies following the smelly RMS, we'll surely find a way around when will get to it. Now, after mjg wrote a long technical pieces about the struggles of making Fedora boot on UEFI with Secure Boot enabled, we can the alarmists were right and Microsoft managed to give a fatal blow to Free Software on the desktop with the help of many hardware manufacturers.
The problem is Free Software won't be able to co-exist with Windows and keep its freedom, people will have to make the choice: break-up totally with Windows (really hard in the computing landscape of today) or give away one of the fundamental freedoms granted by GPL (modify and distribute the software). Sure, this is not a problem in the server world, where you can safely turn Secure Boot off and live happily (boot malware does not affect Linux) as this is not a problem in the enterprise desktop in the places where the game is Linux-only. It is a problem in the hobbyist space, where people play with different stuff all the time and is a problem with adoption, when new potential users will have their computers locked to Windows. It is also not a Linux problem, is a Free Software problem, if you give away freedoms, you can still run Linux.
Rest here