Fantasmic! absolutely costs more to run than they take in from dining packages. It is an expensive show, with a lot of performers, techs, GSO cast, pyrotechnics, etc. Even without a dragon, the operational costs are high. (Incidentally, they've said all along that there would be no dragon upon reopening.)
Keep in mind that when you pay for a dining package, a fair portion of that is truly just paying for your meal - paying $55 for a meal isn't the same as paying $55 for a seat. While the dining packages bring in some additional income and help offset the operational costs, it's definitely cheaper to have zero Fantasmic.
Additionally, they've been rehearsing, paying the cast overnights, for months - I believe since February, in addition to all the costs associated with fixing the show. A lot of the technological elements were damaged by the fire, and they had significant structural repairs and upgrades to do. They're certainly spending a lot of money to bring it back to the parks. And I'm glad! I love Fantasmic!