It is, ultimately, a cry of victory. The Lord's Anointed One (Messiah) will come to save and deliver his people at last. In the present time, however, it is a cry of desperation, "Save us now, Lord! How long will you delay? Come and rescue your people!" This is why the Pharisees were so upset when the crowds greeted Jesus in this way (Matthew 21:15).
Jesus laments over Jerusalem because the Holy City and its people are about to reject God and his promised Messiah. There can be only one way for Jerusalem to be saved now. Its people must come to a place where they know only desperation, and in that desperation, cry out, "Blessed is he who comes in the name of the Lord!"