Depends on how the biomass is generated, but stuff that was just going to decompose anyway, like pig slurry, might as well be processed into a form that can be burnt for energy.
Capturing and burning the methane "downgrades" the potency of the emissions, now only emitting CO2.
Also, if done sustainably, you have to keep sustaining life forms that keep doing the photosyntesis trick for you every year. i.e. All those carbon atoms in this year's crop of Christmas Trees were in the atmosphere a couple of years ago, and we are potentially breathing out at least part of the crops from the next few years... But if someone goes and cuts down a big chunk of the Amazonas in order to make "bio-fuels", yeah, that's dishonest, stupid and self defeating.