My point is that the science you all put your faith into deems this reality to be nothing but materialism and physical matter.
Faith is antithetical to science.
What is the problem with materialism? You're really hung up on everything being physical when it's such a trivial detail. We are "just" matter. That doesn't mean we don't feel, that doesn't mean we aren't alive.
So as someone else eluded to, according to your best scientific theories the only reason human beings care or feel empathy to one another is because it's helpful at propagating genes and DNA blablabla. That's literally what some other dude made it out to be earlier in this discussion, it simply makes us out to be nothing more than biochemical machines right?
Yes. Notice though that despite being biological machines we still care for each other.
My point is that I believe there is a greater purpose to everything including our suffering,
Greater purpose seems unlikely. It is possible that there is more to the world than we currently know, but unless that can be proven the idea doesn't do much for us. It's also potentially dangerous to hold on to such ideas if they get in the way of understanding what is actually going on.
that we feel empathy for others because we have souls or rather we are souls simply in physical vessels.
Your explanation does not tell us anything. You could just ask why do souls feel things? Oddly enough if souls did exist and were required for emotions, the reasons why could go back to something like evolution. That would at least provide us with information that we could use to better understand the world, as is the case with the study of real evolution.
If someone asks "why do people make judgements based on appearance?"
Evolution can provide an answer, visual similarity may be a stand in for genetic closeness, and knowing this it might be a good idea to remember people that they have a bias that is influencing their decision making. The result of that is hopefully a more fair world to live in.
What are we supposed to do with the idea of souls? Nothing more than the physical world is required for love and empathy.
Say we see a wounded animal and feel a natural urge to help it, but why? Does it help propagate and spread our DNA in any kind of way? No
Humans have lived with animals for millennia. Cats can protect our stored foods from infestation. Dogs can guard our homes. Horses provide transportation. Helping animals does help us.
Though you also have to remember how evolution actually works. The passing of genes and increase in survival rates is something that happens on a population scale, not an individual one. Altruism helped and continues to help us, and so it was one of the things passed on from our ancestors. As a result we are still altruistic today. No one confronted with a situation actively thinks about how to manipulate the situation to better their odds of passing on genes. Evolution does not have a goal, nor does it enforce a goal on living things.
it's because animals are beings (souls) just like we are and so we naturally feel an urge to help that goes beyond logic, an urge that comes from the heart/soul.
More information is needed here. The souls seem totally irrelevant. Maybe if they were defined this would make a little more sense.