In some cases, they might have had a less than pleasant experience when they were first contacted by explorers or loggers. Nowadays, while they'd be in danger should they meet illegal loggers and the like, it shouldn't be dangerous for them to contact the authorities. However, their memory from the initial encounter might have been passed on for generations.
Also, as you say, the Brazilian agency in charge of documenting and protecting the Indians has a policy of not forcing contact. So those tribes can remain uncontacted indefinitely.
The page below has more info. Use your favorite translator.
http://mundoestranho.abril.com.br/materia/ainda-existem-trib...
Perhaps more interesting is the case of the Sentinelese, who live on islands in the bay of bengal, and may have had literally no spoken contact with outsiders in hundreds of years:
http://www.uncontactedtribes.org/brazilfootage