The church fathers teach that St John is not raising his own doubts, but is gently guiding his disciples to seek an answer to their doubts. For what it's worth, Martin Luther agrees. However, an existentialist reading (i.e., projecting what we would do, seeing ourselves as St John, making ourselves the subject of the inquiry), which became common after the Reformation (see Kierkegaard, et al.), suggests that St John is not so pious as to be above doubts and fears; in fact, to deny the possible doubts and fears to St John is to deny his "humanity" and, perhaps, call into question his need to be "saved from original sin" (assuming, of course, that original sin is the primary thing from which one needs to be saved).
In his characteristic manner, a friend offers a clear view of the "question behind the question" (i.e., which tradition is running one's hermeneutics).
As in so many other questions, it’s hard to separate an honest and open exegesis of the text from what we have theologically at stake in the answer. What is at stake here is: “Is John the baptist freed from original sin on this side of glory?”
You can see that the traditional answer to that question is Yes by looking at the Calendar. Only three people have liturgical celebrations of their physical birth: Jesus (Dec. 25), Mary (Sept. 8), John the Baptist (June 24). Normal saints are celebrated on their death days - their heavenly birthday... As explained in Weiser’s Handbook of Christian Feasts and Customs, that John and Mary get additional days for their physical births reflects the church’s ancient belief that Mary and John were cleansed of original sin before birth: thus John can leap in the womb and be full of the Spirit even there, and in Mary’s case, many believed that she was preserved from original sin altogether. ...
So, that’s what is lying behind this argument for many people. If you are invested in John being cleansed of original sin in the womb, you simply cannot understand him to be wavering in doubt. If you are invested in John being “just another sinner” then you will really want to jump on this verse as “proving” your point.
But I do not think that this verse can profitably act as a fulcrum to pry an opponent into one’s own camp. One’s opponent reads this verse (as oneself does) in light of a prior commitment: is John cleansed from original sin in this life ahead of the Consummation?