My knowledge of the Black Panthers is really limited, but it seems that it was an organization that focused its activities almost exclusively in the urban areas of the East and West Coast, particularly Oakland and New York City (and to some extent the Midwest). I'm reading through Bryan Borrough's new book, Days of Rage, and he does mention that the NYC chapter of the Black Panthers did move for a time to Tennesse and then Florida, but these were temporary safe-havens after gaining attention from police in New York. So, why would the Black Panthers not have a major presence in the American South, where racism seems to have been much more ingrained in society and politics (not to discount the racism prevalent in the North)?
In Mississippi, at least, they allegedly had a presence in Port Gibson but would have been enormously outnumbered and outgunned by a power structure that included legally sanctioned forces like the Sovereignty Commission, a state government body that existed to keep tabs on "potential troublemakers" (and who kept a file on the Black Panthers along their files on other groups like the NAACP), and, on the other hand, officially unsanctioned vigilantes like Byron de la Beckwith, who shot NAACP organizer Medgar Evers in 1963 and was convicted of murder... in 1994.
His trials in the 1960s ended in hung juries. In order to serve on a jury, you had to be able to vote, which meant that in Mississippi, you were probably white. (Remember, the folks who got murdered in the Mississippi Burning case were down there registering people to vote. That was dangerous, front-line stuff in 1960s Mississippi.)
Beckwith was a member of the White Citizens' Council, a group that... well, it's a little hard to explain, but was both formally constituted, out in the public and well-organized, but also... non-governmental and informally constituted. Meaning: Just because you subscribed to their newspaper didn't mean you were necessarily a member. Just a citizen, you know. Concerned with states' rights and the Southern way of life. (Those are code words, in case you missed that. And that last link should maybe have a trigger warning.)
So if the Sovereignty Commission needed some information that the state police couldn't really get because of privacy laws, say... well, maybe some folks in the Citizens' Council would be able to add some informal observations to the secret files. And some of their members overlapped with more violent organizations that were off the official radar.
Evers' murder (and the murder of the three civil rights workers) wasn't really all that out of the ordinary for this time and place. You could have two white men take a 14-year-old boy from his great uncle's home, beat him to death, be identified in court by the great uncle and other witnesses, be acquitted of murder after an hour of deliberation (would've been shorter but we stopped for a cold drink, one juror said), then confess in a magazine article, "Yes, we killed him!" and not face any repercussions (other than a black boycott of their businesses).
Mississippi wasn't like other places, maybe. And maybe into the 1970s, it might have been different. In the 1960s, though, I don't think a really active revolutionary group would live too long.
Also (and we're creeping a little away from what I've read up on), in Mississippi and the South, it seems like most civil rights organizing took place in churches. Not sure how well that would sit with the revolutionary Marxist element of Black Panther ideology.