These three power lines are almost certainly not the only lines to the Machine City. We know that the population of the Matrix is about 6.5 billion, which means that the surface area to house all the human bodies plugged into the Matrix would be substantial. Indeed, Morpheus says that the fields of humans are "endless":
There are fields, endless fields, where human beings are no longer born.
The Matrix (transcript)
Such "endless" fields would likely require many more power lines from each field to the Machine City -- the three power lines shown in The Matrix Revolutions would therefore constitute only a small fraction of the total power delivered to the Machine City.
Furthermore, Neo and Trinity saw those power lines at a highly unusual time: almost the entire Sentinel army was attacking Zion, and Zion was about to be destroyed entirely. Under more normal circumstances, the power lines would have been guarded by Sentinels. The machines probably opted not to leave any Sentinels behind to guard them because (a) sending more Sentinels to Zion would increase the machines' chances of achieving a victory, and (b) the obvious strategy for Zion would be to keep every ship near Zion to defend the human city itself rather than try to attack the machines elsewhere. Neo and Trinity only managed to encounter these undefended power lines because Neo was thinking outside of the box.
Moreover, the machines evidently have considerable energy storage -- the Sentinels (which number at least a quarter of a million) are obviously not directly connected to the human power source -- therefore the destruction of the power lines would not shut down the machines immediately even if those three were the only power lines. It would take time for the loss of the power lines to affect the machines, and Zion did not have time -- its destruction was imminent. The machines could have finished off Zion and then tasked Sentinels to repair the power lines before they ran out of energy.