I did exactly this trip some time ago and it was a dream. Leaving from Sao Paulo to Santos, following the coast Caraguatatuba, Sao Sebastiao, Ilha Grande, Ubatuba, Paraty and Rio de Janeiro. I haven`t noticed any security problems.
My only serious advice: void driving in the city. Spend a nice day or two in Sao Paulo, go my Bus or Cab to the Guarulhos Airport, get a car there and leave directly. You do not have to cross the city and immediately can enjoy the beautiful landscape. When you get to Rio, leave the car in the Airport e.g. and spend some days in the city afterwards.
You should definitely stay a day or two in Paraty, absolutely beautiful. If you want to drive back from rio to SP you may take the other route and pass by Maua, a small place in the mountains of Rio with some beautiful waterfalls.
I plan on repeating this some time soon too.