Chuck Smith discusses the reasons why prayers may go unanswered, emphasizing that sin in our hearts can create a barrier between us and God, as stated in Psalms 66:18. He explains that God's inability to answer is not the issue; rather, it is our own separation from Him due to sin. Additionally, he highlights that sometimes we do not receive answers simply because we do not ask, or our motives may be selfish. Smith encourages self-examination of our hearts and motives in prayer, reminding us that true prayer seeks alignment with God's will.