Specifically with respect to the methane cow farts, yes. That carbon comes from their plant diet (be it grass in a field or grain in a feeding lot), and the carbon in those plants came from the atmosphere.
This isn't counting the fossil fuels the industry also burns, or the carbon released during the production of fertilizers used when growing that feed. But the carbon in the feed itself all comes from the atmosphere, and therefore the carbon in the methane emitted by cows comes from the atmosphere.
