I saw it as a religious song about redemption and the emptiness of evil. About fatigue and about hope in simple, direct manner. And about reconciliation with yourself in the look forinner peace.
But, sure, first it is a Bob Dylan.
You discover him lyric by lyric and sound by sound and the virtue of pray has, for this motif, special nuances.
In simple definition, supperficial off course one, a classic. For his admirers , more. For message and for used symbols, for cultural references and for the atmosphere inspiring it.
A song about Heaven and about presumed salvation ? Maybe ! More important, a song about hope and love. A powerful one, no doubts.