I think your argument would be stronger if you only ate animals that you hunted (maybe this is your position, correct me if I'm wrong). In that instance then it is possible that maybe the 'survival is the fittest' mentality stands, but I would like to offer two responses.
First, if I am incorrect and some of the meat you eat is not from free chase hunting, I don't think it's fair to say that it's the animals job to survive. Many animals in factory farms are born into those conditions with no means of escape. They have no possibility of matching wits with you and them coming out on top. These animals are doomed from the beginning, they cannot survive even if they tried. I don't think it's a fair characterization of their situation.
Second, even the survival of the fittest argument seems to me to be morally bankrupt. If you are to assume that humans are higher on the food chain, I don't think you would hesitate to say that humans also have higher cognitive ability (the ability to rationally deliberate, etc) than animals do. Please note that I also think that many non-human animals have those abilities too, but that's not where I'm going with this. My argument is that if we can assume that humans have higher cognitive functions, can't we also assume that humans have the ability to ethically make decisions on a higher level than non-human animals? Couldn't one of those decisions be to not eat meat? It appears to me that your argument really gets you nowhere, and that the idea that we are better than them is a reason to NOT eat animals, rather than to do so.
Sorry if this is convoluted I'm doing crazy amounts of homework so I probably rushed my response a little bit.
Whether we hunt or not is irrelevant. I certainly could hunt, but courtesy of one of our fantastic adaptations called specialization, my time is better spent on other endeavors. We're talking about species food-chains, not an individual food-chain, wherein I would certainly rank lower than a terrifying number of animals in the wild. But we've advanced to the point of domesticating and farming animals.
That being said, it is wholly the job of the animal to survive. Who else would be in charge of that? Let's say we discovered an island free from human invasion, and as we observed, we noticed a species going extinct, would it be our duty to preserve that animal who failed in adapting to the environment around it? I don't think so. We let animals eat each other in nature all the time. The issue most people seem to have here is the nature of factory farming, which you mentioned. While I don't think the 'chance of survival' argument holds much weight, I entirely agree that as rational, cognitive beings capable of creating moral codes we should be seeking to minimize the physical suffering of the animals we eat as much as possible.
As for your last part, we can assume that we can make decisions on a higher ethical level, and not-eating meat is certainly a moral decision we can make. But you must see here how YOUR argument gets us nowhere. Because we haven't made that decision. Maybe you have, but that's up to you. Just because we can consider something from a 'higher cognitive' level, doesn't mean that the outcome will go your way.
And I think my argument is a natural one. We require (I guess we could debate this, but that might be for a nutritionist's forum) meat, meat is available, ergo eating meat is morally permissible. From here you are welcome to debate the manner in which we get our meat, but the conclusion remains the same.
Your argument is (I'm assuming here) we can live without meat, eating meat is unethical, we are capable of making this rational ethical decision, ergo we shouldn't eat meat.
Your argument gets us nowhere because it necessarily leads to a moral judgment. And you just haven't given adequate support to suggest that eating meat is not morally permissible.