The pattern I'm using calls it a Throw, but I believe will work as a Crib size. It's 56 x 46 (which will wrap up a baby nicely). Is this an appropriate size? The pattern also includes sizes for Twin and Queen.

I think so. That's about the size I generally shoot for. They grow so fast that if they are made much smaller than that they would outgrow it quickly.

sure-if it's a size you like.
you can make your quilts any size that works for you.
a crib batting measures 45"x 60"

I wouls say about 45x60.

Crib Mattresses are 27x52 and a standard crib batting is 45x60. I think the size you're making will be just fine!

my size rule is "large enough to cover the kid but not to big for the bed".

sounds about right to me. I usually make mine 45x54,sometimes 45x45.