Might I ask how old the babies are? Did the mother sit on the eggs?
From my experience, a big enough snake will eat newborn baby muscovies. They are in danger until they get too big for the snake to swallow.
Rats will also carry off and eat newborn baby muscovies. They will take them right out from under the mother. We put doors made of hardware cloth on our duck condos and close the mothers and babies in at night to protect them.
Of course they are very vulnerable to any birds of prey - hawks, owls, etc. Even bass eat baby ducks. And yes, a drake will sometimes kill a baby duck. A top on your pen will help a lot.
As for the mother, if she is keeping her babies warm when they need it, then she is being a good mom. A muscovy duck doesn't hover right over her babies. They are pretty independent of her from the time they come off the nest (usually when they are one or two days old). They only go up under her when they need to rest or are frightened. She may be being a better mother than you think. Or not. They do teach them, by example, how to eat and to watch for predators. If you have time, really observe your mother duck without her knowing you are there. Then you'll know for sure how she is doing.
******* This is important!! Someone wrote about putting her in with another mother and babies and letting that mother take up the slack. While I have had mothers that stole other mother's babies, I've also had mother's that KILLED other mother's babies. Someone explained to me that she does that to protect the food supply for her own offspring. Now we don't let our mothers be closed in together when they have babies. They are ok if they are free ranging, but we don't close them in together. Of course, when they are free ranging, they are vulnerable to every kind of predator there is.... including cats and dogs. So we rotate ours around a lot. It takes a bit of work, but it is worth it.
Hope this helps a little. Please keep us posted on how Charlotte is doing. And yes, if she doesn't do well with her first batch, she MAY improve with the next one. I have one that just won't take care of the babies no matter what. Many times she abandons the nest after setting almost the whole time. It can be very frustrating. Gotta watch her, so I can grab the eggs and put them under somebody else or in the incubator. Hope Charlotte gets the hang of it.