I am importing already created database in visual studio 2013 from SQL server 2012.
But I am little bit confused about why import permissions and import database settings is by default unchecked.
I think all the settings are important then why this so.
Reason 1: Your database administrator may want to manage permissions and database-level settings directly on the server. (Also see Peter's comment)
Reason 2: Some people like to put database-level settings in a separate database project. This is useful when you have multiple databases on the same server, each having its own database project, and you don't want to duplicate the scripts for the logins & settings in each project. (That's how the pre-SSDT database projects worked. You'd create a server project for the server-level stuff in addition to your database projects.)