The would-be Capitania do Rio de Janeiro was an area known for the fiercely independent natives. The only tribe that got along with the Portuguese was expelled to São Tomé/Espírito Santo, afaik. Portuguese control of that area was tenuous at best. It took 7 years to kill the surviving 20 Frenchmen, after all?
Only because the colony was destroied in 1560 and Mem de Sá was stupid enough to believe that the Frenchmen who escaped wouldn't be a problem. If he had left even a minor garrison in Guanabara they wouldn't have survived.
About the tribes, while Araribóia was the only who supported the Portuguese, all the other tribes soon were defeated or changed their alliance, as showed by the fate of the Tamoio Confederation. It was basically because the Jesuits as Nobrega and Anchieta were already succeding in convince the natives to support the Portuguese.
Maybe if they are well entrenched in the area, they'd be less bothered, I don't know. If the colony survives until the XVII century, it could very well survive longer. Maybe it could benefit from the 80 Years War and the Dutch-Portuguese War?
Well, I agree that if they had survived until 1590-1600 they could have a chance. After all, when the Dutch invaded the Northeast later they were expelled more due to effort of the Portuguese population already living there than due to Portugal's help. And Rio wouldn't be a valuable colony by then, they probably could be let alone.
However, if you don't change the fate of France, I think the best chance for France Antartique would be if it becomes a Catholic colony rather than a Protestant. They could then have more support from the king and more colonists. IIRC the French government would forbid sometime later the immigration of Protestants to Canada, and I believe the same policy would be used in the South American colony. Also, they could use French Jesuits to make the same job the Portuguese were doing with the natives, converting many tribes or even convincing the converted that the French were better neighbours than the Portuguese.
I wonder how would be the situation of the Capitania de São Vicente, isolated by the rest of the Portuguese colonies by a French enclave in Guanabara.