First of all: I am a mother of 5 small children, and a breeder of Cockapoos. From what I have seen, most children are only scared of animals if their parents are. Could she of happened to see you react jumpy with the pup?
Normally unless something happens to a child, such as being attacked by a dog at a early age, most children are not inherently afraid of animals. Children will react the very same way you or your husband react (to anything-storms...thunder even).
I am not saying that You-yourself are actually afraid of your new pup, but for some reason your actions could have made her uneasy with him. You cannot act jumpy or nervous around the pup, even when your children are not around. They see everything.
Always tell your daughter she is so brave with him or great with him, and such, and she will have more confidence.
I have found that sometimes, pups are just overly aggressive at first because they want love all the time. Your new pup will need to find where the boundaries are, (such as-not on the couch, or only on the bed at night) before he gets to be 6 months of age. After that, they are a "teenager" and are done learning rules for the most part.
Now, a good trainer can train any dog, but as for me, a soccer mom. I have to start them early. We actually have our children hold the pups from day one.
Oh, and the more you have him locked in his pen or kennel, the more excited he will be each time he sees your daughter when he gets out. He will be calm, if he is free- calm after about 30 minutes that is... he will just sleep at her feet hopefully after that.
Have a day where he can roam free, as long as your home can take it, and you hopefully will find a calm little pup inside that ball of energy, that scares your little girl.
Good Luck, and remember, Your puppy thinks he was bad when you put him in his kennel, or pen so reserve that for when he eats her new crocs.. which he will....oh fyi...for a chewing dog try cheap pacifiers for chew toys.
N.