Preventing installed apps from making calls or sending SMS
The only right advise here is to download an app with the same functionality but that does not grants itself this permission.

Developers sometimes grant their apps permission their app in fact doesn't need. If you are aware and you don't agree with this trend, the only thing you can do is not download such apps. 
Or even better, you can consider contacting the developer of the application and ask him why this permission is required. Maybe they are not aware of the fact and are very willing to remove the permission if they can please their users with it.

A to-do list should not have the permission to send SMS messages, if I see a to-do app that requires this permission myself, I would just look for another app to use.