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I think the general idea is that one could use the flag to signal something you wanted to work on, regardless of when it might be due. Go through your projects in the morning, flag the stuff you want to do. Then pull up the context mode view, select "due or flagged" actions and grind it out. That gets you all of the stuff you've decided is important to get done first, in essence. One might regard it as the OmniFocus analog of Things' "Today" feature.

There were lots of complaints in the past about how it was impossible to get a single view that showed both things that were due and things that were flagged. Omni listened and addressed that need. Reasonable people can disagree about whether such a view should show items which are due but unavailable -- I think it is a good thing, and protects one from nasty surprises, but I can also see cases where I might not want it. Use Help->Send Feedback to send in your request for the ability to control the behavior. The Due Soon filter works the same way, showing actions which are due (soon or already) but unavailable.