Not necessarily. Sure the series quote 'song of ice and fire' is a reference to Jon, but it has many other meanings. It also applies to magic. All magic we have seen preformed, in both the books and the show, are either ice based or fire based. It could also work for what may be the final big conflict of the series. If you are of the mind that the Others (aka Whit Walkers) are not as evil as we have been lead to believe, then the final conflict could very well come down to Ice vs Fire, with major characters on each side. There is a great theory about this, which I will quickly summarize.
Basically, it's the idea that the Others are not the bad guys of the story, we just think they are. Thousands of years ago, there was a war, where the humans and the Children of the Forests (who were magical beings that inhabited Westeros long before Men showed up) fought the Others and there army's of Wights (aka the zombies that can only be killed by being set on fire.) The war was ended when a great hero somehow beat the Others back into the north, and the wall was built to keep them there. The theory states that the war was not ended in some great battle, but rather ended with a sort of treaty, stating that Humans would stay in the south and the Others would stay in the north. The wall was built as a sort of property line, and the Nights Watch was formed to keep everybody on the right side. But that was a long time ago, and humans forgot their side of the deal. Humans started moving north of the wall, to get away from laws and kings, and their descendants are now known as the Wildlings. At one point in the books, a wildling character talks about how the Wildlings are moving south, and cannot stop because the Others are always there, nipping at their heels. They kill a few Wildlings during the night, but never really attack in force. If they wanted to they could wipe them all out, but they don't. They just sort of herd the Wildlings south, towards the wall. They don't care that the Humans south of the wall don't want them, they are just trying to get them off their land. They never really attack in force, until they find humans actively moving north. In the very first scene we see an Other kill two members of the Nights Watch, and leave a third alive, in hopes that he will spread the message. Instead he runs away and is later beheaded by Ned. They attack in force again when the Great Ranging takes place, and more than 200 men go north. Because they are killing Humans, we assume they are the bad guys. But really, they are just honoring their side of the deal, a deal that humans forgot about.
Anyway, back to the ASOIAF thing. It is possible that Jon will discover this treaty, and eventually join the Others in an attempt to restore the peace between them and men. He (and a few other major characters you don't really know about yet) will be on the side of Ice. Dany (and a few other characters you don't know enough about yet) will be on the side of fire. There will be a great battle, Fire vs Ice, where the audience is rooting for both sides because only they know that neither side is the bad guy. Ice sees Fire as invaders come to conquer Westeros, Fire sees Ice as a threat to humanity, even though it isn't. Any series can have good guys vs bad guys, but it takes a series like this one to have good guys vs good guys.
Anyway, point being that Jon is not the main character, because there is no main character. Jon and Dany are likely the 2 most important characters, but I'm sure the others (Arya, Sansa, And Tyrion) will have a major role to play in the final battle as well. But a series has to have a name, and that name fits particularly well.