This isn't a change this is the way it has been for as long as I've been back (so Sept). You cannot target a toon that is in a vehicle, but you can focus that toon.
Works:
/follow toon1
Or:
/focus toon1
/follow focus
Does not work:
/tar toon1
Or:
/assist toon1

There is/was some odd behavior that seems to happen WHEN you get in the vehicle, so sometimes my "follow state" would persist when I got into a vehicle and sometimes it would not.

I just created a more complicated macro that does a targetexact, then a follow, then a setfocus with a follow. I'll put it up later if people are interested - but you can probably figure it out