I tend to say this to others and also to myself when there are challenging circumstances. What I actually mean is that whatever the issue, health, work, relationships or whatever, it is what it is and when I accept the simple reality of the situation, it will be all right. All right in the sense that I will find a way to cope with the difficult reality, I will accept it and simply move forward, no longer allowing it to distract me.
Stuff happens. Bad stuff. Lot of bad stuff. Pain, suffering, the death of all of those we love, job losses, physical and, sometimes, mental disabilities etc. happen. But it is all right because it is our reality and acceptance and not dwelling on the pain is our only option if we wish to move forward. Letting go. Dwelling on the issue increases the pain and leaves us stuck. Looking at it for what it is and simply accepting, allows us to move forward.
I think when people use certain phrases we tend to assume the worst. Sometimes they just mean that they care.