The thing about Sam Wilson is...
He’s not only incredibly empathetic, he’s perceptive. From their first meeting, he’s able to pick up the way Steve shuts down at the mention of being frozen, recognize that Steve has PTSD and reach out to him sympathetically without blinking an eye. He’s willing to take Steve and Natasha in when everyone else is trying to kill them with no questions asked, because he knows they couldn’t have gotten to that place without a good reason. He is able to make Steve laugh, smile, trust him and accept his offers of help, something Steve is doing with no one else, because he figures out the right things to say.
So when Brock Rumlow is telling him that with Hydra, order comes from pain, that Hydra doesn’t take prisoners and Sam tells him to shut the hell up, IT’S INCREDIBLY IMPORTANT. Rumlow is doing a cliche villain monologue, trying to justify his actions and explain his objectives, and Sam SHUTS HIM DOWN. Sam, the perceptive, empathetic character WILL NOT LET HIM JUSTIFY OR EXPLAIN WHY IT’S OKAY FOR HYDRA TO DO THESE THINGS.
That should tell you everything you need to know about whether any sympathy should be extended to Hydra or members there-of in this universe. Sam did not and would not. And Sam, like Steve, is an everyman character, idealized. Sam is all of us, if we were the best we could be. By having Sam say that line, the narrative is indicating none of us should give these characters a chance to explain themselves, because no explanation will make their actions excusable.