Hi Law,
When someone apologises to us, we can indicate our acceptance of that apology with "it's fine". When we feel that the outcome of something is acceptable to us, we can say "That's fine. Don't worry about it."
Example:
They delivered my furniture with a few scratches, but I think it's fine."
It's a way of telling others that everything is alright and you are not bothered with something.
When we are not bothered with either way something turns out, we say "It doesn't matter." The outcome does not affect us or is irrelevant.
Example:
We are not sure which one of our children vandalised the wall. It doesn't matter, all of them will repaint the wall.
You would not write: "We are not sure which one of our children vandalised the wall. It's fine!
Hope this helps.
Lance