It means "how is it going?" and you ask it when you intend to know how is something progressing. Though I've already seen it being used as a greeting, generally the "how is it coming along?" question is made with context (when there is something particular happening during a time). "I see you're writing your final essay. How is it coming along?" would be an example.

I think someone is asking how your progress on a task is going. Perhaps a task mentioned earlier in the conversation or the last time you spoke.