If they are still making a lot of $$ they will still make them.

 

It really depends on TF3.

If it isn't well received, my guess is the producers will back off on the series for a couple of years, and then come back with a reboot (or as they will say "re-imagining") of the Transformers series.
If TF3 does do well, the producers will try to continue it to TF4, and possibly beyond. I know Don Murphy said he wants the Transformers films to end up being like James Bond in terms of a series. However, I don't think that Shia or Bay will come back after TF3. Shia's going to want to do other films, and same with Michael Bay. Shia may have had the opportunity to make a couple movies in between, but will be almost 7 straight years on the Transformers trilogy for Michael Bay by the time TF3 comes out.

Really, only time can tell.