Ask Slashdot: Linux-Friendly Desktop x86 Motherboard Manufacturers?
I only skimmed the "horror stories", but as you said, they seem to be mostly about problems with updating the BIOS. The actual hardware support should work out of the box under Linux in nearly all cases, unless you want to get at really specific motherboard features. If you think you need those, you should know which ones exactly (they are probably the reason you'd chose this particular motherboard), and do some research if there are Linux drivers available.
Asrock offers BIOS updates for "Instant Flash" without an OS (e.g. Z97, random model). When I bought an Asrock motherboard some years ago, they didn't offer this for the particular model I bought, so I emailed their support. They mailed back that the BIOS update could be dangerous for early steppings of this board and this was the reason it was not publicly available; told me how to figure out my stepping, and gave me a link to an "Instant Flash" image I could use at my own risk. Can't complain about this.
So if you are worried about BIOS updates, it works just fine with Asrock motherboards according to my experience.
There's also a tool called "flashrom" that can flash the BIOS directly under Linux, but it doesn't work with all motherboards.