Okay, And So I am developing a site in which a user can make Profiles. I would like the consumer Profiles to become like http://example.com/username but however , it conflicts along with other Rules.

RewriteEngine on
Options +FollowSymLinks
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule story/(.*)/ story.php?id=$1
RewriteRule story/(.*) story.php?id=$1

RewriteRule (.*)/ profile.php?id=$1
RewriteRule (.*) profile.php?id=$1

Now, ultimately that after I attempt to go to http://example.com/story/hello_world The machine thinks that 'story' within the URL may be the UserName and searches for this within the Database after which throws the 404 Page(not surprisingly).

I dont want user pages like example.com/user/username .

Example: Digg.com has digg.com/story and digg.com/username

You are able to replace each of your rules using the rule below to avoid the issue with http://example.com/story/hello_world being construed like a user.

RewriteRule ^([^/])+/?$ profile.php?id=$1 [L]

For those who have more specific rules on username, e.g. username is alphanumeric and between 5-10 figures lengthy, a better rule could be

RewriteRule ^([a-zA-Z0-9]{5,10})/?$ profile.php?id=$1 [L]