I have been to Cape Cod many times- as a child, I would vacation in Eastham with my family and still go every few years. As for running the Flyer during these difficult times, we have to understand that just because the case rate on Cape Cod might not be as high as other places doesn't mean that we are completely out of the woods yet. The greater Boston area probably has a lot more cases than Cape Cod and if that's the case and somebody who tests positive with the COVID-19 boards the Flyer, guess what, the virus will spread to other people on the train and then those people getting off the train could spread it even more. Next thing you know, people are in the hospital and not everyone will make it.
Here in the NYC area where I live, it's horrible in NYC. Several people have passed away already. There is some improvements with the case rate slowing. Unfortunately, a New Jersey Transit rail conductor passed away from the COVID-19. Multiple NYCMTA workers got the COVID-19 and many of them passed away.
As for the Cape Flyer running to the Cape this summer, if things return to normal by Labor Day, I hate to say this but I wouldn't count on the train to the Cape from Boston running. It will just be like a normal year at that point given the fact that children will be back in school so the families who have school aged children won't be heading to Cape Cod at all. That doesn't mean that many people won't to the Cape past Labor Day. For five out of the six years, my family has gone to the Cape in September toward the middle or the end of the month. It's not as busy there as it is during the summer. I don't know what the ridership count would be on the Cape Flyer after Labor Day but it might just get by.