When Proctor says this, he is speaking to Reverend Hale. Elizabeth has been arrested, and the true story of the poppet has been exposed. It is fairly obvious, if you use any sort of common sense, and if you know-as the reader does-Abigail's motives in accusing Elizabeth, that the poppet was a set-up. To Proctor, the fact that Abby saw Mary put the needle there is proof of Elizabeth's innocence. So, he is aghast when they still arrest her and are taking her away. He turns to Hale for help, asking, "Will you see her taken?" to which Hale responds, "Proctor, the court is just." In a sense, Hale is saying that he has no power in this situation, and that Elizabeth was in the hands of the courts. This is where Proctor calls him Pontius Pilate.
In the Bible, when Christ is brought before the courts, Pontius Pilate is in charge. Pontius questions Christ and finds nothing wrong; he feels that Christ is innocent, and has no reason to be arrested. So, he brings Christ before the people, and there was a custom on the Passover where one criminal could be allowed free. Pontius states his case for Christ, and asks the people who they would have be free-Christ or a convicted murderer named Barrabas. The people vote to have Barrabas released, and Christ crucified. Pontius disagrees, but doesn't act to save Christ. Instead, he took up water and washed his hands of the affair, symbolically saying the court system and people have spoken-it's out of my hands. It probably wasn't, and Pontius washing his hands has come to symbolize people doing nothing in the face of a severe injustice, because they are passing blame elsewhere. So, Proctor is saying that Hale has the power to save Elizabeth from being arrested, but that he is cowering behind the "the courts are just, and if she is innocent she'll be released" argument, instead of acting in his own power and right to save her as he should. That is very similar to Pontius washing his hands of the matter of saving Christ, pretending to be innocent in the face of a person being unjustly condemned. I hope that explanation clears things up a bit. Good luck!
As the Roman Prefect of Judea during the years A.D 26 to A.D 36, Pontius Pilate was responsible for ordering the execution of Jesus Christ. Pilate, however, did not want to condemn Jesus, having been warned not to do so by his wife, who had dreamed that nothing good would come from the sentencing of this innocent man. When the Jews bring Jesus before Pilate, he examines him and finds no evidence of wrongdoing, but the Jews are insistent that Jesus should die. Pilate eventually gives in to their wishes, but in the process, "washes his hands" of the matter, effectively assigning the blame to them.
When Cheever orders that John Proctor's wife Elizabeth be brought before the court to answer to charges of witchcraft, Proctor is enraged. He appeals to Reverend Hale, who tries to defend what the court is doing, and Proctor responds by saying, "Pontius Pilate! God will not let you wash your hands of this!" Proctor is telling the Reverend that he cannot be like Pilate, by acceding to the wishes of those who wish to condemn while absolving himself of blame in the matter. Proctor is saying that by going along with what he considers the ridiculously unjust actions of the court, the Reverend too is responsible for whatever should happen to Elizabeth and the others as a result (Act II, Scene 4).