Cantando raises some great points.
Also understand that the manure animals produce is a form of pollution. It can make wells or freshwater sources undrinkable. Unlike human waste, livestock farms have no sewage treatment plant. They store it in massive open lagoons, and periodically dispose of it by spraying it on crops. If a bad storm comes, the lagoons have been known to flood over or crumble.
Waste, animal waste and human health - The Issues - Sustainable Table 
Even "grass fed" animals out on pasture are pooping out raw, untreated, pathogen waste. Then we wonder why there is E Coli showing up on spinach or in household wells.
Runoff from factory farms goes into waterways and results in fish-kills, dead-zones, closed beaches, and long-term damage to fisheries/ecosystems. In my local area, the problem are the chicken waste ending up in estuaries and then the Chesapeake Bay, and the result is pfisteria which causes huge fish kills and is a danger to people. We know these kills trace back to "hot" chicken manure being spread and then washed into creeks, but nobody wants to take action because that would cost chicken farmers money. In Delaware, chicken production is one of the top agricultural products for the state... home of Tyson, Purdue, and a few other industry giants.
Pfiesteria and Chattonella new evidence of linking to animal waste manures Maryland on lookout for next pfiesteria outbreak 
The manure used to help fertilize crops is not clean. Even once the pathogens die off, we still have contaminants. Now they're finding those chemicals being absorbed by the food crops we eat, tainting even "organic" crops:
Crops absorb livestock antibiotics, science shows — Environmental Health News
Ruminating livestock such as cows produce quite a bit of waste gas. A few cows wouldn't matter, but when you're talking billions of cows, it's a problem: livestock produces 28% of the greenhouse gasses released in the USA. And unlike any other industry or individual, there are no pollution controls for livestock farms
EPA - Ruminant Livestock - Frequent Questions
It's a local dirty industry, bringing down local property values and lowering the quality of life for neighbors.
Consider the processing plants (slaughterhouses). Once they cut off the usable meat for butchering and ship the bone and other big bits to rendering, there is still a massive amount of blood, intestinal contents, and other bodily fluids. This is supposed to be well treated before it's released, but the sheer amount & concentration make it difficult. Sometimes the burden is passed to the local community who have to pay to upgrade community sewage treatment plants to deal with all this waste. Sometimes it leaks, is spilled by trucks, is sprayed on open land, or otherwise escapes. Now you've got a biohazard spill on the road in front of your home or leaking into the creek that feeds your reservoir.
One good example we know a lot about were the three horse slaughterhouses (in IL and TX) which were regularly cited for spills and other environmental violations.
Horse slaughter dream could be financial nightmare | Horsetalk - International horse news
Blood spill on public road:
You might also want to read up on the world environmental damage meat production causes. Our hunger for cheap meat fuels clearing of South American rain forests, to make way for cheap soy and for beef cattle grazing. People say they want to save the rainforest, but you can't if you're helping to support those who slash-and-burn the land.
Deforestation in the Amazon
Some other links you may find interesting:
The Impact of Industrialized Animal Agriculture on the Environment | The Humane Society of the United States The Environmental Impact of a Meat-Based Diet http://www.nrdc.org/water/pollution/.../cesspools.pdf Manure The Impact of Factory farms on the Environment Food & Water Watch — Food & Water Watch