Methane production requires nearly a total anoxic environment. Even trace amounts of oxygen are enough for substantial suppression. Decaying roots, even if they were deeper, would be exposed to at least a little oxygen throughout the early decay process (unless continually flooded with water). Once the roots have decayed to a stage where they are more decay resistant, there would naturally be even less local oxygen, but they would also be in a state not favorable for substantial methane production.

The chemistry seems complicated. To create methane, you need hydrogen, which is a byproduct of previous anaerobic microbe activity. Think lots of fresh plant material decomposing in an anaerobic environment.