the real question is are they pathogenic bacteria or symbiotic ones? of course bacteria live in our brain, and viruses too.
if you use a washcloth for a few weeks with warm water, it becomes a nest for bacteria and begins to smell foul.
But what are we to think of ourselves? We're the perfect temperature for breeding; we're practically decades long petri dish experiments.
The bacteria, owing to their size and un-evolved ways, have a much harder time infiltrating the brain than viruses who attach our DNA, and an equally harder time staying put once they establish base. Think of meningitis or lyme disease, do you really think in every case the bacteria made it in through the nose or eyes or some head trauma? The blood-brain-barrier lets in drugs why not bacteria. They have ways of sneaking in too, perhaps they were laying there since inception, dormant, waiting for the brain's defenses to slip up, for a chink in our armor. Perhaps we recover our immunity and the brain puts them back in check, perhaps in the case of lyme disease we are simple outdone in evolution. In either case the brain has not evolved clear defenses against symbiotic ones since symbiotic bacteria have no tendency to harm us and no tendency to multiply or divide out of control like other unwelcome guests
As for the viruses, i believe everyone has some herpes on their frontal lobes. Maybe they don't if they haven't kissed a girl, but even so they got it as a child by sharing a glass of cranberry juice with their mom. I would think the brain has evolved its own proprietary not-quite-strictly-immune defense to such threats, which in old age, often compromises itself and is implicated strongly in end-of-life dementia.
Scientists will look back in a hundred years through a time capsule at this and wonder how we could know all this in 2018. Some will think we're genius, but we're not, we're only very, very smart. Perhaps as smart as you can be without being a full-blown genius. Perhaps no where near. Perhaps it is only opinion and not knowledge, but what then is a well-informed opinion except nothing at all. We draw the inferences we like because all good ideas arrive by chance