That needs context. Hoover considered them the biggest internal threat because he considered them a threat to the social hierarchy. He heavily opposed Civil Rights and designated any such groups championing those causes a large threat. So, it's not that they were considered the biggest internal threat because Americans, Congress, etc. felt them to be so. They were considered so by the FBI because Hoover didn't like the idea of black people and white people being treated equally.
In fact Hoover's biggest gripe with the Black Panthers wasn't guns or even cops who were murdered. His biggest gripe was with the Free Children's Breakfast program.
Why? Because he saw it as some sort of way for extremist groups, ie Civil Rights groups, to infiltrate communities with their propaganda.
So, Hoover's assessment of why they were a threat isn't the same as what you're applying it to.