I think you have your Rewrite rules inside your default server, at the top level.
Add another level to your Rewrite rules, such as adding "^ez3/" ahead of the match value (the second field on the line), where "ez3" is whatever you want the eZpublish site to be called. http://localhost/ez3/index.php, etc. eZp3 will look for the "index.php" part of the URL to find the file paths.
Or use virtual domains and have your rules within the appropriate domain definition.
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