(Image courtesy of http://realitychurch.com.)
What does one make of the phrase: “God answers prayers, but not always the way we want Him to”? This phrase, often quoted by Christians, reveals two things: 1) God’s ways are not our ways, and 2) we do not trust God.

If the Christian truly knew God and, as a result, trusted in Him - that His ways are always good and that He “works all things together for the good of those who love Him and are called according to His purpose” (Romans 8:28) - then we would not say that God did not answer our prayers how we wanted Him to. Instead, the surrendered, regenerate believer should be able to say confidently that God has answered my prayers to my good and to God’s glory every time with 100% accuracy.

We should not think that God answers us with evil or ungoodness. Jesus taught that even an evil man will not give his son a rock if he asks for a piece of bread, and that God will much more give us good things if we ask Him (Matthew 7). God always answers prayers to the good of His people and to the glory of Himself.
If we knew Him, we would know that He is working in us for good, in conforming us to the image of pure goodness - Jesus Christ Himself: "For those God foreknew, He also predestined to be conformed to the image of His Son..." (Romans 8:29). 
If we knew Him, we would also know that He is working for the glory of Himself: "... that He might be the firstborn among many brothers" (Romans 8:29).
According to the story of Job in the Bible, by chapter 38, Job and his friends had spent more than thirty chapters debating why God would do or allow these horrible things to happen to Job. His family was killed, his crops and cattle were destroyed, and his own body was severely afflicted with disease. After all human wisdom was expended, God intervened, saying through the whirlwind, “Who is this that darkens counsel by words without knowledge? Now gird up your loins like a man (prepare yourself and be ready), and I will ask you, and you instruct Me!” (Job 38:1-2).  Did Job or his friends understand or know what God’s purposes were in allowing these things to happen to Job? After all their efforts, they were no better off understanding God's purposes. God demonstrates to them in the following chapters that they are man and He is God, that they have no wisdom in comparison to His. He is Sovereign and nothing happens apart from His purposes, even if man questions and wonders what His purposes are.

So, in light of who God is - namely, He is Sovereign and good and perfect in all that He does (Deuteronomy 32:4) - the Christian's response should be one of rejoicing and trust, not vain questioning and darkening of His counsel with words without knowledge.  Therefore, let us study and know the one true God and submit our minds and hearts under He who is the Head.  And let us pray, as Jesus prayed, "let Your will be done."

"He is the Rock, His work is perfect: for all His ways are judgment: a God of truth and without iniquity, just and right is He" (Deuteronomy 32:4).