What does John 6:64 mean?

Sadly, not all people who "follow" Jesus actually "believe in" Jesus. The story told in chapter 6 is a vivid illustration of this unfortunate truth. Crowds gathered around Him due to His miracles (John 6:2). They were so impressed by His feeding of thousands that they were ready to make Him a king (John 6:15). And yet, when Jesus explains that entertainment and free food are not His real ministry, they are unimpressed (John 6:41). The more He insists on a spiritual, personal meaning behind His miracles, the angrier they become (John 6:52). Eventually, as the next verses will show, many of these shallow "followers" will leave, proving they are not "believers."

There is a profound difference between being attracted to some aspects of Christianity, versus actually being a born-again Christian. Typically, the difference is shown when a Christian message conflicts with a person's preferences. In this case, most of the people hearing Jesus' message don't like it, and that causes them to abandon Him. As Jesus said in the prior verse, "the flesh is no help at all." Actions which are not grounded in legitimate spirituality are pointless.

Peter, on the other hand, expresses the attitude of an actual "believer" in Christ. Namely, that whether He likes what He hears or not, He knows that Jesus is the Truth (John 6:68–69). Instead of rejecting Jesus because Jesus challenges his thinking, Peter submits to a higher truth than his own.

Here, Jesus is speaking to His "disciples" in a very broad sense. In context, this term refers to all of the people who have been tagging along and listening to His teaching. The core group of twelve men, on the other hand, will be specifically addressed after many of these other "disciples" turn and walk away.