I know rabies was once considered 100% fatal, but now has some survivors due to the Milwaukee protocol. Are there any infectious diseases that have a 100% mortality rate?
Creutzfeldt-Jakob disease is considered 100 percent fatal.
CJD is classified as a contagious disease because it can be transmitted through contact with contaminated tissue during medical procedures. But it's not spread through the air or by casual contact.
And this link describes how CJD was transmitted during medical procedures.
However, rabies does have survivors though they are mostly impaired. Survival requires intensive medical care. There are about 15 cases in India as of a couple of years ago, and several well publicised American cases.
First a clarification: The Milwaukee Protocol is now considered a failure. As a treatment option it not considered valid option any more.
There are vaccines for rabies and port exposure prophylaxis treatment is available but it still has a a very bad prognosis and if left untreated or with treatment started too late is fatal:
Rabies is an almost invariably fatal disease that can present as classic furious rabies or paralytic rabies. Recovery has been reported in only a few patients, most of whom were infected with bat rabies virus variants, and has been associated with promptness of host immune response and spontaneous (immune) virus clearance.
A similar picture presents Human African trypanosomiasis:
Human African trypanosomiasis or sleeping sickness is a neglected tropical disease that affects populations in sub-Saharan Africa. The disease is caused by infection with the gambiense and rhodesiense subspecies of the extracellular parasite Trypanosoma brucei, and is transmitted to humans by bites of infected tsetse flies. The disease evolves in two stages, the hemolymphatic and meningoencephalitic stages, the latter being defined by central nervous system infection after trypanosomal traversal of the blood-brain barrier. African trypanosomiasis, which leads to severe neuroinflammation, is fatal without treatment, but the available drugs are toxic and complicated to administer. […] No vaccine being available, control of human African trypanosomiasis relies on diagnosis and treatment of infected patients, assisted by vector control. Better diagnostic tools and safer, easy to use drugs are needed to facilitate elimination of the disease.
Then there is the old classic, the plague in two of its sub-forms:
Yersinia pestis and plague - an update: The plague of man is a severe, systemic bacterial infectious disease. Without antibacterial therapy, the disease is associated with a high case fatality rate, ranging from 40% (bubonic plague) to nearly 100% (septicemic and pneumonic plague).
Another contender is the rare but also almost deadly parasite Naegleria fowleri causing primary amebic meningoencephalitis (PAM) — amebic encephalitis:
What is the fatality rate for an infected person who begins to show signs and symptoms?
––The fatality rate is over 97%. Only 4 people out of 143 known infected individuals in the United States from 1962 to 2016 have survived.
Is there effective treatment for infection with Naegleria fowleri?
––It is not clear. Several drugs are effective against Naegleria fowleri in the laboratory. However, their effectiveness is unclear since almost all infections have been fatal, even when people were treated with similar drug combinations. Recently, two people with Naegleria infection survived after being treated with a new drug called miltefosine that was given along with other drugs and aggressive management of brain swelling.