The Methane is generated from chemical reactions involving what they eat. The corn they're fed frequently in the US (because of our massive corn subsidies) makes them worse than they would normally be. No matter what though, they expel what they take in. The carbon for the Methane is gathered by grass from carbon dioxide in the air. Methane breaks down relatively quickly back into CO2. It's mostly a non-issue if it were done in a healthy way.

Again, we aren't and won't be doing it sustainably (at a large scale), so this is all a thought exercise. If you were to raise cattle yourself on land that doesn't otherwise have a use, it'd be carbon and energy neutral. It's all a part of a system. Humans break that system, but cattle don't need to. They only do when humans are involved.