Secure Boot is almost certainly not causing you problems yet
There's been a few links to this story of someone buying a system that turned out to have UEFI firmware and also turned out not to boot. Given all the press, it's unsurprising that people would assume that problems they have with UEFI booting are related to Secure Boot, but it's very unlikely that this is the actual problem here. First, nobody's shipping an appropriately signed operating system yet. A hardware vendor that enabled secure boot out of the box would be selling a machine that wouldn't boot any OS you could buy. That's a poor way to make money. Second, the system booted a Fedora 17 CD. Fedora 17 isn't signed, so if the firmware booted it then the firmware isn't enforcing Secure Boot. Third, it didn't boot the installed OS. That's really at the point of it sounding like a hardware problem - selling systems that don't run the OS you sold them with is a guaranteed way of getting enough support calls that you wouldn't make any money on them, ever.
To be fair, Linux compatibility with UEFI systems is still not as good as it is with BIOS systems. Fedora 18 will be using a new UEFI boot process and so far in our testing it's been significantly more reliable than Fedora 17. There's still some remaining issues that we're aware of and working on, but right now it's hugely more likely that failures to boot Fedora 17 on UEFI systems are down to our bugs rather than Secure Boot.