When looked at this way, the most sensible suggestion is that this is Clark pouring out his feelings to his long-time crush, Lana Lang (Kristin Kreuk). This fits because, like many heroes forced to keep their heroic secondary lives hidden from most people that are close to them, Clark is often lonely and angsty throughout "Smallville" and is pining to share the truth with some of his friends, especially Lana.
In this way, "Save Me" joins the ranks of other Superman-related songs like "Kryptonite" by 3 Doors Down and "Superman (It's Not Easy)" by Five For Fighting in suggesting that America's greatest superhero may need some saving of his own. Furthermore, when you consider that Superman eventually goes dark at some point in almost every version of the mythos, including "Smallville," this makes a lot of sense.
While most of Clark's friends and a few of his enemies would eventually learn the truth of his secret identity, he was never able to get his happy ending with Lana. Still, he did wind up meeting and falling in love with his classic canonical love interest, Lois Lane (Erica Durance). Even if the romance had a long build-up, the two finally got together in the final seasons of "Smallville."
