It's not just that biomass "seems" natural. It absorbs carbon dioxide while it's growing, so the CO2 released when it's burned would be absorbed by the next crop.
That said, it's certainly true that some ethanol production has a negative energy balance. Corn isn't particularly suitable for ethanol. And, in the US, corn is very energy intensive to produce.
I understand that sugar-cane is much more efficient. The stated reason, here in Brazil, for shifting towards ethanol, was to become more self-sufficient and to avoid further oil shocks after the 70s. I'm not sure about the amount of coal available here, but I'd imagine that that goal would have been invalidated if there was a net energy-loss, and growing ethanol had used more imported oil than it substituted. I guess here it has a (maybe small) positive value.