This has happened to me many a time, but I know the short routes quite well - so I either quickly ask the driver to use the short-route turning if it doesn't seem like he's going that way - or mention when we arrive that I know there was a shorter route, tell him the usual price, and often they're nice enough to give you the difference! Don't feel like you're nitpicking - it doesn't seem like much at the time but it adds up to a lot if you use taxis frequently.
Obviously this will mean getting to know the route a little better - checking out Google Maps before a journey usually gives you the shortest route, remember the street names and see if the driver takes them.
Perhaps try to always use the same taxi company - getting in random ones in taxi ranks can throw up some surprises in terms of how much they charge you. If you know the company's average price for the distance, you can quote that to them!