For a disease to make us go extinct it would have to be highly transmissible and have a fatality rate of close to 100%. Anything less than that, and evolution will produce a generation of humans that are resistant to (or otherwise able to protect themselves from) the disease, and from there the population will replenish itself. The great plague had a fatality rate of 30% and it didn't even come close to threatening our existence as a specie. (In fact, the resulting redistribution of wealth arguably contributed to the advent of the renaissance.)