Right now, if you make a reservation online, it might. Take a look at the total amount due today. If that says "$0.00", then your card will be used as a hold. If it has an actual dollar amount, then it's telling you it will be charged.
Now there are two ways to go about this. The first way is to book over the phone. The CM over the phone can manually enter that you have a dining plan and thus force the system to recognize it and have you only use a hold. Or, you can continue and book online, paying upfront, to be reimbursed when you dine.
This is caused by an issue in the website where it won't always recognize that you have a dining plan associated with your room reservation. It's been happening more since the change in systems, but is an old bug.