In the end that was the choice you made, and it doesn't matter how hard it was to make it. It matters that you did.

This quote is referring to a difficult decision that someone had to make. It is recognizing that it was tough to make this decision, but emphasizing that it is more important that they did in fact make it. It is saying that in the end, the person made a choice and the fact that it was hard to come to that decision is not as important as the fact that they actually made a decision.