This is used when you're not 100% sure you will be able to do something, but you strongly predict that you will. For example:
I'm sure we can work something out.
This means that you think you will be able to find a solution to an issue.
This means that you think that your store will start to get a lot of customers again soon.
This phrase is useful in situations where you want to reassure the listener. Or it can also be used to threaten someone like in the example at the top. In this case, you're saying that you strongly predict that the person you're threatening will agree with you, because if they don't, you will do something bad to them.