The feed links that are included in the HTML code depend on your theme. For example, Twenty Ten only includes one feed type (with two feeds: posts and comments). Check your header.php to see which feeds are referenced there.
If it is a modern theme (like Twenty Ten), you might see no feed links there. This is because WordPress calls feed_links() in wp_head, which will (if the theme supports automatic-feed-links) output links for posts and entries in the default feed format, which is rss2 if you don’t change it via the default_feed filter.
Additionally, on some pages like category archives, feed_links_extra() will also output links for a feed for only that category, again in the default feed format.
If you really want to disable a feed (so requests for example.com/atom will no longer work), you can do something like two7s_clash suggested, or play with the rewrite rules so atom is no longer part of the allowed feeds.