"not really"
 

1)I really don't like it.
2)I don't really like it.

Are they the same meanings or not?

I think either (number one and two) or (only number one) can means "I strongly don't like it."

And number two can means either "I just like it but not much." or "I strongly don't like it."

Re: "not really"
 

1) Really has falling intonation and "amplifies" don't, so the meaning becomes I don't like it at all.
2) Really has fall-rise intonation and "downtones" like, with the meaning I don't like it very much

Quite is another adverb which has this dual, and apparently contradictory role of amplifier/downtoner. See this thread for more info.

Re: "not really"
 

1. I really don't like it means you hate it

2. I don't really like it means you don't like it very much, if at all.