This is a common question. Having the site's root as the top result for a site: query is not guaranteed and nor is it a sign of a problem if it's not. It just so happens that in the vast majority of cases we return it as the first result.
Barry Schwartz of SE Roundtable blogged about it and his post generated a discussion on Google+: https://plus.google.com/107945426404682361496/posts/Fa8Vgwe1xj7
Hope this helps,