This article strikes me as very poor for a number of reasons.

1) It ignores that there are strong arguments against eating meat that are committed neither to utilitarianism nor to the existence of animal rights (1, 2).

2) It's not at all clear what the author means by saying that "Singer argues that any being that suffers has full moral status." This is false, at least if we take "full moral status" to mean the same moral status as typical adult human beings. Singer famously argues that newborn babies, for instance, lack the moral status of adults. And of course, Singer doesn't think that we owe the same considerations to a cow as to a human being--he just thinks that, insofar as each one has an interest in not suffering, we're prima facie obligated to respect that interest. The fact that one is a cow and one is a human being has no moral relevance to those obligations.

3) The author assumes that, if we do buy Singer's utilitarian arguments, we should be committed to the repugnant conclusion, and hence to thinking that we're justified in causing untold amounts of suffering to animals, just as long as we raise enough of them. This assumes that utilitarians must be concerned with total utility, and not average utility, in a population. But this assumption is false.

4) The author asks, "if suffering is bad then according to utilitarianism it does not matter whether the suffering is caused by disease, accidents, predators, or overcrowding in stockyards. Why then is human-caused suffering worse than the suffering animals endure in the wild?" But who is committed to claiming that human-caused suffering is worse than suffering in the wild? We're responsible for the suffering we cause, and we shouldn't cause suffering. The existence of suffering that we don't cause can hardly justify our causing any suffering we want, regardless of whether the suffering we don't cause is greater or lesser than the suffering we do cause.

5) Actually, the author has a kind of answer to that. He says the following:

Yet, many utilitarians including Singer seem indifferent to the suffering of wild animals, focusing only on suffering caused by raising animals for food. Granted, when animals are killed for food they are killed intentionally. Animals killed by predators, disease, or the building of human settlements are not killed intentionally. But intentions are not supposed to matter for utilitarians; only states of affairs matter.

First of all, it's false to say that "intentions are not supposed to matter for utilitarians." Utilitarians would have us act in a way that we could reasonably expect to produce the most happiness (or whatever it is that your specific theory of utilitarianism tells us to produce). It's not like we're praiseworthy if we drive drunk and accidentally crash into Hitler's car, or something. And second, intentions don't even seem to be the matter at issue here. It's not like we intentionally cause cows to die on farms, but accidentally cause gazelles to die when lions eat them. We don't cause the gazelles to die at all!

6) Citing one study of Australian agriculture is hardly sufficient to establish the thesis that eating plants causes as much suffering and death as eating animals. Especially as most livestock raised for meat are fed on plants we grow, in most cases it's almost certainly true that eating plants causes less suffering.

7) The author performs some self-described "speculation" on animal psychology to conclude that animals probably don't mind suffering very much. Where on earth this conclusion comes from I don't know. As has been pointed out many times, there's no obvious reason to think that greater higher-order cognition will always be associated with greater suffering (or greater badness of suffering).

8) Near the end of the article, the author turns to metaethics, saying this:

Morality is not a set of principles written in the stars. Morality arises, because as human beings, we need to cooperate with each other in order to thrive, and such cooperation requires trust. The institution of morality is a set of considerations that helps to secure the requisite level of trust to enable that cooperation. That is why morality is a stable evolutionary development.

This position is at least contentious, probably false, and not argued for at all. If we need to argue for this position to deny that we have obligations not to cause animals to suffer, then by all means argue for it--but the author hasn't done that here.

9) Apparently realizing that his position might commit us to thinking that we're free to do whatever we please to animals, the author slips this point in at the end:

This is not to say we should be cruel to animals, lack empathy for them, or ignore their welfare. The reason is not that they have rights. Rather it is because cruelty is a character flaw that we should strive to overcome.

It's not exactly clear what the message is supposed to be here. It's either a kind of statement of virtue ethics--in which case, if we can dismiss utilitarianism for being controversial, surely we can dismiss virtue ethics as well--or else it's merely saying that, while some mistreatment of animals is acceptable, "cruelty" is not. But what exactly constitutes cruelty seems to be at least one of the matters at issue here, so just asserting that raising animals for meat is not cruel is question-begging.

10) Finally, the author appeals to our limited "moral energy":

The humane treatment of animals is one among many moral projects we should undertake, but it has no special priority over the many more pressing human needs that cry out for our attention.

This is simply dishonest. No one is saying that we should ignore human suffering and focus on animal suffering instead. Not eating meat is not some huge undertaking to which we must commit hours out of our days. It's just something we don't do. It's about as easy as not holding slaves or not committing rape.