The Shulchan Aruch HaRav (quoting the Taz) says that a Chazzan should pray from the communities siddur, since it was written for Hashem's sake.
However, he says, that if the siddur is printed there is no difference between siddurim.
One can learn this two ways:
Since the main Kedusha falls only though handwriting (for example, a chumash [or Tikkun] doesn't have the same rules as a Sefer Torah), there is no real difference between "holy" publishers and "un-holy" publishers.
Since there were only a few printers, one can assume that they were all printed with the same intent. Therefore, if one is bad so are the rest. If so, even if the siddurim don't have the proper holiness, there is nothing one can do about it.
This case could be a practical difference.
If the first way is the correct way, then (possibly) one may learn from works published by kofrim. If the second way is correct, then one should still look for books written by holy Jews.
However, the Tzitz Eliezer quotes a Chazon Ish who says that modern printing works differently than the printing of a few centuries ago.
Back then, every print was done with direct human power. Therefore, there is still some (inherent) Kedusha in printed works. Nowadays, when one just presses a button and the printing is done automatically, unless the works are made for learning, one may destroy them by hand.
Therefore, it's possible that even according to the second interpretation, one may be able to learn from those books.