what did Atticus mean when he said " The one thing that does not abide by the majority is a person's conscience?"

A person's individual conscience is not decided by the majority. Whatever the jury conclude, it doesn't necessarily determine the truth and Tom will know whether he is guilty or not, meaning he determines his own conscience as guilty or innocent. As well as this, whatever the jury say, that doesn't align with the whole town's opinion or Atticus' opinion, and Atticus will know he's done the right thing in defending Tom and the town doesn't have to agree with the jury's sentence.