they want $200 for a cab from rome to the port for 2 people.
I hate having to lug my luggage--but can I get a cab at the port train station to the ship? I've read they aren't necessarily waiting around.
Yes, $200 is about right. A taxi from the airport to Roma is about half that, and the airport is about midway between.
Have your travel agent contact your cruise line and inquire about the cost of the cruise line's transfers. Most cruise lines do offer transfers between Roma and Civitavecchia for travellers with "independent arrangements" ending in Roma before the cruise.