Recommended modules for managing Content access?
Recommended modules

Here is what I consider as the "shortlist" for such modules (quotes are from their project pages):


Content Access.


  This module allows you to manage permissions for content types by role and author. It allows you to specifiy custom view, edit and delete permissions for each content type. Optionally you can enable per content access settings, so you can customize the access for each content node.

Taxonomy Access Control:


  Access control for user roles based on taxonomy categories (vocabulary, terms).
  
  
  Automatically controls access to nodes (based on their taxonomy terms).
  Configuration page for each user role.
  Three node access permission types: View, Update, Delete.
  Two term access types: View tag, Add tag.
  

Simple Access (RC4 version only for D7):


  This module allows administrators to make some nodes private and/or editable by certain user roles. It can manage viewability, editability, and/or deletability and provides an easy way to make nodes accessible by only a group (or groups) of users. It is perfectly suited for making private nodes that are only viewable to certain 'access groups'.
  
  Access groups are based on roles. So for example, my site has roles entitled "Coach Level 1", "Coach Level 2", and "Coach Level 3". I can create an access group called "Coaches" and assign all of these roles to it. Then when I assign a node to be viewable only by "Coaches", only users who are a member of these roles will be able to view.
  
  Nodes that are not assigned to any access groups will remain viewable by all users, so all nodes will remain viewable when activating this module. And nodes only become private when they are assigned to an access group. The end result is that this module can be enabled for a site with existing nodes without making them all invisible.



Special case: Organic Groups, which provides 'Groups' for Drupal users, and management of Access Control based on these groups. A great resource for learning about Organic Groups is the (free) video training about Learn Organic groups, a set of 14 videos.

My "recommended" module is Content Access ... Also because of al sorts of integrations with the Rules module.

For more details, refer to Access Control modules.

Rebuilding permissions

About "Rebuild permissions": any time the "Access" rules are changed (via admin settings), Drupal needs to ensure that these rules are applied to all impacted content (nodes). That's why Drupal then re-applies the updated access rules. A special case is the "installation" (actually "enable") of a module, when rebuilding permissions is also required. Makes sense? Clear enough?