Pythagorean wins is a formula that uses runs scored and runs allowed to see how many games you deserved to win. It's not an exact science, but if there is a large difference between this win percentage and your actual win percentage, you might have a lot of luck involvement.
This is not the case with the Cubs, who are a medium run scoring team and a terrible run prevention team. This formula says the Cubs deserved to win about 39% of their games, which is the actual number.
That doesn't mean the Cubs haven't been lucky or unlucky. I'd say they are unlucky, mostly due to injuries being worse than most teams. However, it's wrong to think the Cubs haven't played like a 20-games-under-.500 team.