The idea is not to get hit with a VTOL, that's true. However, depending on the era and optional rules (not a lot on my part), that can be arranged. Combined arms doesn't mean, your VTOLs should be out in the open. Quite the opposite, actually. Usually, VTOLs will be able to generate very high TMMs. If you let your opponent shoot at another target that is easier to hit, but more resilient, which would he choose,
I must admit, it changes a bit, once you start moving around BA. They might actually be better off with APCs than with VTOLs as those generate a "too many eggs in one basket" situation too easily. On the other hand, fast-moving BA across the battlefield could be done in a light OmniMech like the Owens (IS) or Dasher (Clan).