drupal /?q=user is working but /user not working
As you have checked mod_rewrite settings for your server and .htaccess both it sems that you may have mis-configured  RewriteBase in your .htaccess file.

Please check comments in .htaccess file

# Modify the RewriteBase if you are using Drupal in a subdirectory or in a
   VirtualDocumentRoot and the rewrite rules are not working properly.
   For example if your site is at http://example.com/drupal then its value should be:

RewriteBase /drupal


If your site is running in a VirtualDocumentRoot at http://example.com/,
   then its value should be:

RewriteBase /


Try and see if you have something wrong here.