It can be in a plugin. In fact, F J Kaiser added a comment to the Codex page a couple weeks ago (with no explanation) implying using it in a theme could be problematic.
This probably because a recurring event should be scheduled only once, such as during plugin activation. Doing so from functions.php will result in a redundant scheduled event being added for every WP page requested!
Note that you could put the scheduler inside a conditional that checks for the existence of a schedule already with wp_next_scheduled(). In such a case, scheduling from functions.php should work OK.
