It's worth noting that as late as 2006, Clinton was saying she "had no plans" to run in 2008.
At the present time, Clinton is very focused on her current job. But what will her mindset be in 2015? If the Obama Administration is unpopular and/or her term as Secretary of State is widely regarded as a botch, she will likely stay in the "not running" category. But if her position and the political environment looks at least somewhat favorable, I think her future is open for debate.
Clinton is unlikely to even be Secretary of State in 2016. The attrition rate for cabinet members is very high. Only one of Bush's 2001 appointees, Elaine Chao, made through his entire Presidency; just three of Clinton's did. Clinton has a higher public profile than most cabinet members usually do, but I still find it unlikely that she will not have shuffled to another job or left the administration entirely by 2016.
