It is not known why only a small proportion of people infected with a virus develop meningitis. For most of the viruses that cause meningitis, the proportion is actually as small a 1 in 100.
Although it is not known for human infections, in animals, there appears to be a genetic susceptibility to developing meningitis. The first step in any virus infection is attachment of the virus to the surface of the cell. The virus must attach to a very specific protein on the surface of the cell in order to be able to enter the cell. If it cannot attach to the cell, it can get inside and multiply. It appears from the animal experiments, that some animals do not make the specific protein receptor on the cell surface so the virus cannot infect the cells of this animal. The same may be true in the human viral meningitis infections. Only a small proportion of people may have the receptor protein that allows the virus to enter cells in the lining of the brain to cause meningitis.