If there are a lot of cows, yes, it might harm the atmosphere. Cows and other grazing animals lay out 78000000000 kilograms per year of methane. If people start eating more meat then this will increase to about 79000000000 kilograms per year within about 20 years. Humans put out 1000000000 kilograms per year of methane too! This doesn't harm plants directly but scientists think that large amounts of methane can help cause global warming. This can harm plants.
The gas can cause global warming by capturing energy from sunlight and keeping it in the atmosphere as heat. Eventually so much gas captures enough energy that global warming results. Some good web sites are
http://www-cger.nies.go.jp/grid-e/gridtxt/grid9.html ,
http://www.unfccc.de/fccc/ccinfo/senegal/fact/fs271.htm , and
http://www.towson.edu/polsci/ppp/sp97/globalwarm/methane.htm

Cows do produce lots of methane gas as a byproduct of eating grass which has cellulose in it.Cows, like humans are not able to digest cellulose so they employ special bacteria to do it for them. A byproduct of this reaction is methane gas. When a cow releases the methane it is usually quickly diluted by the open air environment in which it lives, therefore the concentration is so low that it will not adversely affect plants. However, there is some belief that there are so many cows being raised for human consumption now that the amount of methane they produce might be having a noticeable impact on global warming. Methane is a greenhouse gas (see previous questions on pollution from cars).

Hi cow fans - Methane is a problem because it is a greenhouse gas. What happens when you close all your car windows on a summer day? It gets really hot in there right? If you leave the windows open, it's a lot cooler. Pollution such as methane can form a layer in the atmosphere that doesn't allow heat to escape, just like the windows trap heat in your car. This is called the "greenhouse effect". Many scientists think this will lead to global warming. Others aren't sure. How would global warming affect plants and animals?

These sites have more information on the greenhouse effect :
http://www.enviroweb.org/edf/ishappening/greeneffect/greenhouse_howalter.html
http://solardome.com/SolarDome2.html
http://www.nafi.com.au/faq/greenhouse.html

Thanks for asking.