For your sake, I hope you are able to nip this in the bud, immediately. I don't think that $5 is totally insane for the 1 hour in the morning. As long as you don't need to feed him, or drive him to school or even take him to the bus stop. A 9 year old shouldn't really need anything from you during a short period of time so early in the morning. Give him a book or whatever, and that should be enough. But what about PD days, or holiday days? Are you going to be watching him then? I would not be surprised if mom springs that on you in the next little while. And you need to charge her your full day rate!! You will be feeding him and entertaining him the whole day at that point, so no discounts.
You need to hammer out an arrangement that is suitable for payments, ASAP. It is waaaay too easy for someone to walk away from a childcare provider and leave them unpaid. In my area, it is completely common for payment to be made in advance. I would not offer care otherwise.
I would not allow a daily call to mom, for all the reasons stated by yourself and others. Just let her know that you are busy with various activities, and that sometimes it actually makes it difficult for the child to talk to mom. Most of the time, this type of request has everything to do with the parent, and nothing to do with the child.