An important difference being that the WBC are intentionally setting out to disturb the peace. They get all up in your face, as close as they legally can, determined to make sure you hear them whether you want to or not.
Someone carrying a rifle in JC Penney is not adversarial if done right. He's just there, going about his business, and some people are freaking themselves out over a falsely perceived threat. The knowledge that people will freak out in this manner doesn't make it his responsibility.
For an analogous example, say I walk into Harlem, at night, wearing a KKK costume. I correspondingly get assaulted. Now one can argue that it was incredibly stupid for me to walk into Harlem wearing a KKK costume, but that does not make me responsible for the assault. That fault lies with the assailants.
Likewise it's not his fault that people are freaking out over his rifle, it's theirs. They could choose to ignore it, or notice it and then continue going about their business, but the mere fact that there's someone who visibly could threaten them freaks them out.
That's the crux of the issue as I see it. People want to feel safe and secure by whatever means. If you visibly violate that security, they freak out. This is despite the fact there are numerous ways to invisibly violate that security, ways many people encounter on a daily basis, but don't care about; because they aren't visible. At its core, freaking out over a slung rifle seems to me to be a simple matter of human irrationality, and irrational behavior should not be encouraged.