Kneeling in prayer and the liturgy has a complicated history. The First Council of Nicaea (A.D. 325) included a canon proscribing kneeling on Sundays and during Pentecost, suggesting that kneeling was common in the early Church at other times (e.g., on weekdays). Eventually kneeling became more common in public prayer with the increase of adoration of the Blessed Sacrament.
The early Church saw kneeling in public as essentially a penitential act, since the penitents knelt during the parts of the liturgy that they were allowed to attend. Kneeling now has more of a reverential than penitential connotation attached to it.
In regards to the first Christians and Jews not kneeling, we see Peter and Paul kneeling in prayer in Acts 9:40 and 20:36. Likewise, the Jews knelt on the occasion of a special solemnity, as we see when Solomon dedicated the temple, "kneeling down in the presence of all the multitude of Israel, and lifting up his hands towards Heaven" (2 Chr 6:13).
In the Eucharist we are invited to approach an even greater manifestation of God's presence--the literal body, blood, soul, and divinity of God the Son--so it is fitting that we adopt what in our culture is one of the most reverential postures. Most fundamentally, kneeling at the consecration is a matter of obedience. Some may like to stand, but the Holy See does not allow for this (GIRM 21).
If someone argues that we should copy the supposed practice of the early Church, point out two things: (1) The current rubrics don't allow us to stand during the consecration, and (2) if they're really advocating a return to the early Church's practice of the liturgy, that still wouldn't result in everyone at Mass standing. In the early Church, those who had committed grave sins were often required to do penance for years, either outside the church door on Sundays or--if they were allowed in church--kneeling or prostrating themselves through the service while everyone else stood.