Your generator can operate just fine without the cover. But, you need to get another one from the manufacturer because it is part of the noise baffling system and the noise will not just irritate yourself but your neighboring campers.
FYI: If your new RV has sat for a long period of time the fuel filter for the generator may be partially gummed up from sitting with fuel drying up in it.
I would look under the chassis where the RV generator is mounted, and you should see a fuel pump/filter combination there. Get the model number and purchase a new filter to see if this is why it isn't running properly.