I think the very reasons Sydney suggests are among the reasons it's now thought extremely unlikely to impossible that the congregation would have joined in. Or at least that Bach would have intended them to. The congregation may well have sung chorales, perhaps supported by whoever wasn't singing in the cantata at that service (he only used one voice per part in the cantatas the vast majority of the time) but if they did it wasn't in Bach's cantatas but elsewhere in the service. Of course the chorale melody would have been an old friend for them to recognise in the middle of Bach's music in any case.
Besides the fact that Bach often had little instrumental bits between the chorale lines in his concluding settings (think of the last chorales in parts 1, 4 and 6 of the Christmas Oratorio) sometimes there are also slight variants even in the melodies which are set 'simply' and the congregation wouldn't have known they were coming.
The keys chosen are also not always the most friendly for congregational singing. Wachet auf goes up to a G. Ever heard a congregation try and give that note a go?