Port charges most certainly haven't gone away. What the deal is, is that in most cases port charges are now rolled into the per person cost for the cruise. This has a lot of history, most of it involving legal cases in Florida, and the major cruise lines agreed to include port charges in the quoted price per person, but this would not include other fees and taxes. I have no way of knowing your specific situation without seeing the invoice. I can say with a high degree of confidence that you are not being ripped off and whatever is on your final price is valid.
This may be another example of why it is best to use an agent instead of booking on-line. An agent can explain each line item.
Changes can happen to a booking price, often without any control by the cruise line. Alaska for instance has tacked a fee on each passenger by law. RCI and the other lines have no choice but to pass this cost on to the consumers.