Disclaimer: Do not confuse me for an iOS expert. Just got my iPhone.
That is my impression. However, there could be several routes shown. And after seeing what route Apple Maps will create, the route can be indirectly changed by touching the map along the way you really want to go, which will cause a purple pin to drop on the map. Now you can navigate to the new point and then from there, navigate to your destination.
Note, even with dedicated GPS units you have to be careful about setting waypoints and I rarely use them. For example if you use a larger city that includes a beltway, you would not want to have downtown set as a waypoint, unless you specifically want to see downtown.
For the local experts, is there a better way to do (suedo) waypoints using Apple Maps?
This is something I found on my DC-NY trip as well. I wanted to take a particular route that was not one of the 3 options shown.
I doubt Apple will add an option to customize your route (doesn't seem in their MO), but you could either ask it to "navigate to purple pin" and then "navigate to destination", or simply start driving on your route. It will adjust.
I would be nice to ask it to avoid certain areas, but then again, if you want a full-fledged navigation system, you are probably better off with a 3rd party option.
edit: Waze says they learn users' preferred routes. I wonder if Apple has this built in also. Could be a simple option to go on a "preferred" route, instead of one of the 3 automatic ones.