PETA is bat shit, they usually express it by doing really wonderful things like firebombing cancer research clinics where they use animals for research. They are pieces of shit basically.
As to why animals are treated cruelly, it's obviously not malicious I doubt the people running this industry are sadists it's just a question of price. If they treated and slaughtered them more humanely then it would be more expensive and you'd have to pay more for your food. Meat is already one of the more expensive components in a typical healthy meal for a middle class family, making it more expensive is not a good thing.
There are alternatives like free range or organic meat. They cost like three times as much.
Oh and if you want your meat to at least be killed humanely you could take a look at kosher meat, it's more money but not crazy more, and to be kosher it needs to be killed in a certain fashion. I think the same goes for Halal and it's even cheaper as its somewhat less stringent and it's a larger market (in most places).
