Sefer Kedushas Levi states that when Hashem sends pain and suffering, it is actually are beneficial for a person. While the situation appears bad, it is actually good. However, one cannot see the Divine kindness with his human eyes.
He compares this to a doctor that cuts into a person’s body to perform surgery. He appears to be causing suffering to the patient, but he really is healing him.
Accordingly, the pasuk is saying that whatever Hashem does is surely good and one should accept that even things that appear bad are really for his benefit.