"Maybe it is all for the best" suggests an over all good outcome 'sum total." It will have some good for you, but mainly the world will be better off some how... or "lets try to find the good things in this bad situation." It is said when something kind of bad happens... The maybe lets us know that it is going to be hard to find this"good" the speaker is talking about.
The "your" best would probably not be used. If it were used, it would be taking away the "sum total to the world" aspect, and focussing on what may be good about a bad situation on a single person scale. It might be more likely that a different set of words be used for such a situation:
Maybe this will end up best for you in the end.
It was not meant to be.
Look at the bright side....
Something better will come along anyway
When one door closes a window opens