Just because they are asking you to update your payment method, does not mean they are charging you for free apps. They are not going to charge you for a free app, however the Store uses your payment method to further identify you and ensure that you have permission to access the Store that you are trying to use. Just update the method and you should be alright. You can try to change the method to None, see this. Change or remove your Apple ID payment information - Apple Support
If you cannot select None, see this for an explanation. If you can't choose None when you edit your Apple ID payment information - Apple Support