Christ said "on this rock [Himself] I will build My church, and the gates of Hell shall not prevail against it" (Matthew 16:18).
That is one of His first mentions of the church, and He is warning that the gates of Hell will by conspiring to destroy it. Does that sound like a comfortable place to be?
Jesus gives more teaching on the church in chapter 18 of Matthew where he describes it as a family, which should be a comfortable unit. But Jesus decides to focus on an uncomfortable issue of family life, dealing with conflict which can even lead to the exclusion of one of the family members.
"Moreover if your brother sins against you, go and tell him his fault between you and him alone. If he hears you, you have gained your brother. But if he will not hear, take with you one or two more, that ‘by the mouth of two or three witnesses every word may be established.’ And if he refuses to hear them, tell it to the church. But if he refuses even to hear the church, let him be to you like a heathen and a tax collector. (Matthew 18:15-17).
I have had the sad privilege of seeing this carried out, and it is anything but comfortable. Often when this happens, people leave the church because they feel uncomfortable. Tough times like these call us to reflect on why we go to church at all.
So what is the reason for being part of His church that Christ gives? It's simply His presence, "For where two or three are gathered together in My name, I am there in the midst of them" (Matthew 18:20). Christ will be found among the small groups that are dedicated to following His word. They are often excluded from mainstream Christianity (a contradiction in terms if ever there was one). He is among the two or three's that seek to follow Him. Following Him and meeting in His name alone involves rejection by the masses, persecution, and hardest of all, self denial. "Then Jesus said to His disciples, 'If anyone desires to come after Me, let him deny himself, and take up his cross, and follow Me. For whoever desires to save his life will lose it, but whoever loses his life for My sake will find it'" (Matthew 16:24-25).