It sounds like you've already figured out what I was getting at...
It's OK to drill though normal rafters, but you really don't want to be drilling though trusses without permission and specific instructions from the engineer who designed them.
A normal rafter functions as a beam, which means that right in the center there's a dead area where there is very little stress. The top of the beam is in compression, the bottom in tension, and somewhere around the middle the force goes to zero. So it's OK to drill there, because it doesn't effect the strength of the beam.
A chord of a truss works differently. The whole chord is pretty much uniformly under compression or tension, depending on where it is in the truss. If you drill a 1" hole through a 2x4 chord, you've reduced it's strength by almost a third. That's a really bad thing.
