The sentences do have different meanings. See the following EXAMPLES. (These are only examples of how the sentences can be interpreted but it depends completely on context, for instance, when, where, who is speaking, and to whom they are spoken.)
I only teach you. (meaning merely)
Can be taken to mean: I am merely your teacher. You must strive to understand what I teach. Or You must take what I teach and use it. Or I cannot take credit because I am merely (only) the teacher.
I teach only you.
This usually means I have no other students. Or You are the only student who understands. But this second possibility is not normal for this sentence. I mention it because when said that way, the teacher would continue on with more information.
I teach you only.
This sentence seems incomplete or is phrased by a non-native English speaker. I would normally expect to see this sentence continued with something like: I teach you only what I know, or I teach you only what you can understand. These express a limit to the scope of the teaching, instead of limiting how many are taught. Also: I teach you only until you go home. Or I teach you only enough to help you pass the test. As you can see, each of these limit the material taught.
If the last sentence were spoken by a non-native English speaker, it could mean any one of the above possibilities, because non-native speakers tend to change the location of words within a sentence to match how they speak their first language. In that case the student should seek clarification from the speaker. I would be inclined to think the speaker means to use it in the first context since it was not followed by limits, and there was no mention of other students.
So, to recap with EXAMPLES:
I only teach you. means I am merely the teacher.
I teach only you. means I have no other students.
I teach you only. means There are limits to what I teach you.
I hope this helps clear up some confusion.