I was reading in John 16:1-15 this morning. It's when Jesus was telling His disciples that He would be leaving them. He also issues some warnings as to how the disciples will be treated in the future.
It is for our good that Jesus' physical presence went away, because now we have the Counselor, the precious Holy Spirit who guides us into all truth (John 16:13) speaking the very words of God. Jesus did all of this to assure us that one we would have right standing with the Father because He knew that we would never meet His perfect standard. He also wants us to know that we will never be without His presence, no matter how bad our circumstances may seem, we will never be alone!
Our faith cannot be shaken or destroyed by our circumstances, our faith has to be in someone who is stronger and more solid than the shifting sands of our emotions, it is to be in the One who promised, never will I leave you, never will I forsake you.