You can get around that by setting up a system of relays, but you will end up needing lots of relays, and that's a complex infrastructure you need to maintain.
In any case, even after we master inter-stellar travel, don't think we'll have channels of communication of terabytes/second, every byte will be expensive to send across.
Sending information in the quantities needed to 3d-print stuff at atomic level will most likely be prohibitively expensive; remember 1 gram of hydrogen contains 10^23 atoms, while one terabyte only contains 10^12 bytes. If a little latency is acceptable, it will always be many times cheaper to just send the stuff you need rather than the information to 3d-print it at atomic level.