Using this admittedly inadequate amount of information, it is worth conjecture that the brain is responding differently when a person is either meditating or hypnotized and the role of the conscious mind versus the subconscious mind differs. Also, many beginning meditators complain of difficulty controlling the ever-willful subconscious mind. Since both levels of the mind are operating for a meditator, the goal is to establish a very conscious control over what both the conscious and the subconscious mind does. In hypnosis, there are no real control issues so long as trust is established with the hypnotherapist. The therapist focuses the conscious mind entirely on a relaxed state while allowing the subconscious mind to work as it will.
Meditation allows more control over the mental processes and is a form of self-discipline.
Hypnosis can be used to aid self-discipline but is not necessarily something that requires such discipline. These practices are indeed different, although it is difficult to prove what processes occur to make them different. Power of the Witch.