I don't know much about hilchos z'raim (agriculture-related law), but from the mishnayos I recall as follows: If one acquires produce from someone who cannot be trusted to tithe, then he must take the "first tithe" (maaser rishon) from the produce, as well as others, but not t'ruma, the initial tithe that goes to a kohen. This is because everyone, even those who cannot be trusted to tithe in general, can be trusted to take that tithe.
Yet I find that nowadays people do take t'ruma. In fact, the standard tithing text (in various versions that I've seen in prayer books and elsewhere) says to take t'ruma. Even if it gives separate instructions for what to do in case of tithing out of doubt (where tithing is only likely and not surely necessary, i.e. where one acquired the produce from an unreliable source rather than, say, grew it), those instructions do not say to skip taking t'ruma.
Obviously, something has changed over the years. What is it? Was there a decision made at some point that people are no longer trusted to take t'ruma? If so, when and by whom was that decision made and accepted? Or, if not, then what happened to cause the common practice today that people take t'ruma from produce acquired from someone not trusted to tithe?
