Every request sent to the server will send all cookies that have been set for this domain, such as the sess_id cookie. So if you're users are logged in, you could for example do it like this.
css.php
<?php
header('content-type: text/css; charset=...');
// start session. get user data from where it's stored: in $_SESSION, db, ...
?>
body {
background-color: #FFF;
font-family: <?php echo $font; ?>;
}
But remember that browsers cache css files, so if a user makes modifications it will not show in his or her browser unless they clear the cache. So you might want to
echo '<link rel="stylesheet" type="text/css" href="css.php?time='.time().'"/>';
And if you want to separate user modifiable styles from the hard coded parts, keep two files, one with hard coded values and one with user defined.