We are server management provider so we used to charge for the site management. We used to provide free daily backups. Dedicated IP has cost associated with it.
You can charge for the services which are really cost you.
I would not charge for any extras like WHOIS privacy, SSL-s. Basically, anything that is free for me anyways.
On the other hand charging for managed services is a good idea as it takes a lot of time and effort to manage both servers and accounts.
I provide all the required addons with the hosting and don't charge extra for any of it. However I charges for extra IP address, extra Disk Space, provide free migration service.
I try to build a basic package which includes most features (weekly backups, SSL), but for anything that has an additional cost I would charge for. Example extra backups have a cost associated with them (in terms of hard disk space), if a customer needed a dedicated IP there would be a cost associated.