The materialistic approach states that everything can be explained by the laws of physics, and all is caused by the interaction between the particles which compose all things. This approach is mostly accepted by the scientific community, and I believe most atheists accept it.
Considering this approach, the suffering is nothing but chemical and physical reactions that occur in the central nervous system, not to mention that the animals themselves are just a bunch of particles that are not greatly different than the air itself.
On the other hand, if you consider this approach, you can justify killing and torturing of humans, even on massive scales. By this approach, everything is meaningless.
So how can we know what is right and what is wrong? Isn't mortality just some invention of our society to match our feelings and instincts? And if so, how can we tell what is moral and what's not?
So, is suffering of animals bad? I don't think you can answer this question using rational thinking. For me, it is rational that animals are just particles that move somewhat together, and after they die the suffering they have gone through doesn't matter at all. Still, on the same basis I can conclude that it is rational to think that we too have no meaning, and I can torture someone, kill him or maybe kill myself if I feel like, and it wouldn't matter at all. I don't do it because I fell this is wrong. I don't want to be killed; I feel empathy when I see someone else is suffering and even animals suffering. When I eat meat, I don't feel any empathy towards the animal that it once was. I believe this feeling could be changed by the knowledge I acquire and the memories I have. For e.g. some people may acquire this empathy towards the animals that are eaten by them when seeing footage of how meat is produces. Others may need to go to the slaughter house itself and see it in their own eyes. Others may never be affected by those things.
This is why I believe no one can determine if it is moral to eat meat or not, and therefore first issue of eating meat (1) is fully subjective, and can be change between people and even in different times in the same persons' life.
The health issue, as much as I can conclude from my own research, is highly controversial. it seems like there are health benefits in being a vegetarian or vegan, but it is also clear to me that the argument in the subject, and even scientific researches about is, are somewhat biased in accordance to the believes of the author. I did see a stronger evidence that support that there are in fact health benefits to being a vegetarian, and even more to being vegan, but those benefits are not very significant, and are probably very affected by the fact that vegetarians are much more aware of their diet and health than omnivores, and thus eat a well-balanced, healthier diet regardless to the presence of meat in their diet. There are some articles about the benefit of eating less meat, and we can also conclude it from the fact that animal products are the sole source of cholesterol in our diet, and a big source of fat, two things that are known to cause health problems such as cardiovascular diseases.
In conclusion, I believe a self-aware non-vegetarian can make his diet even healthier than an average vegetarian diet (and of course by adding sport you can always be healthier). I do think lowering meat consumption is advised.
An article about vegetarian diet health implications:
therefore, the moral issue is probably the sole issue that should be considered in becoming a complete vegetarian (I consider the economic issue less relevant, due to the controversy on its effectiveness, and the small probability it will be the main reason for someone to become vegetarian). Due to my conclusion that this issue is fully subjective and depends on the persons feelings and unproved believes, I conclude that the vegetarian issue as whole is subjective.
I myself decided to stop eating meat in Mondays for health reasons, as an opportunity to reducing meat consumption and raise vegetables and fruits consumption.