I usually pick a feature that I have some kind of preconceived notion about how big it should be and base my scale on that. For instance, on this map I'd probably choose that brown sandbar, or perhaps the water channel that breaks up the road.
I'm awful at gauging distances, though, so I usually have to base my measurements on known quantities, like the average height of a man or the width of my living room. On at least one occasion, I set my scale based on my desired travel times and then reworked everything else to accommodate that scale. At least one country wound up being much, much larger than I had intended, so I gave it a secondary population of nomads to justify the enormous land area.