When you initially log in, a new shell process is started. You already know that, but what you may not know is that this new shell process (typically bash) runs using your user id. As such, the bash program can access all files and directories that you own. In fact, we as users we are totally dependent on other programs to perform operations on our behalf. Because the programs you start inherit your user id, they cannot access any filesystem objects for which you haven't been granted access.