The charging port does not have a protective cap, because the unit is completely waterproof. We decided not to use a cap because they can fall off on rough terrain, or get lost when charging on the road or in the home - we looked at some solutions here, which were not fitting enough for us and in the end decided against it.
Just like the rest of the bike, the charging port needs a little care from time to time, e.g. with an old toothbrush and some multi-purpose oil. What it does not do well with are metal objects or metal brushes, and it should be dry before the charger is connected.