I think people are having a hard time putting themselves in the shoes of the Fox News people. They are aware that the Serpent Society is an evil hate group, they don't mistakenly think the characters in the comic itself are real conservatives. What they are upset about is that an evil hate group is being shown espousing beliefs and rhetoric that actual, real life conservatives are espousing right now. The comic is implying that the beliefs shared by many normal conservatives are the kind of thing an evil hate group would believe.
Imagine if Marvel released a comic where Captain America had to defend some conservative Christians from being killed by an evil hate group (this hate group is also wearing snake costumes, just to keep the metaphor consistent). And this hate group keeps talking about "structural oppression," "internalized racism and homophobia," and when Captain America tries to talk them down peacefully they say that he is "microaggressing" against them and trying to "silence" them whenever he criticizes something they do. I think a lot of people would be upset because evil murderers are being portrayed as having the same kind of beliefs that many normal nonviolent people on the Left espouse.
For that matter, I seem to remember people being upset that in "The Dark Knight Rises," Bane adopted the sort of rhetoric that the Occupy Movement frequently used. People didn't like hearing their political beliefs coming out of the mouths of supervillains. Actual Occupy people didn't like being portrayed as violent killers.
People can go on all they want about how the Serpent Society aren't real conservatives, they're an evil supervillain hate group. But I think we all know what is really going on. By having an evil hate group say the exact same kinds of things that real conservatives do, Spencer is trying to imply that normal everyday conservatives are evil and hateful.