Can I password protect an entire section in Unity Pro?

Yes. If you right click on 'Project' from the project browser and 'Properties' then the protection tab you can set protection as active and add a password. In the project browser again, you must now right click on the section and from the general tab select 'No read & write' for protection. You will notice that the section is now locked. To unlock it, you must go back to the project properties and turn off the protection by entering the password.