Logos4 isn’t a “bible study” program. It is, however, a very powerful research engine. Yet, this engine needs resources to do its magic. Thus, whatever Protestants might do with the program such as cross indexing, complex etymological lookups, interlinear research, use of concordances and commentaries can be accomplished with Catholic resources as well.
There certainly are some quirks regarding some Protestant resources that are built in. However, an email from the Catholic Products Manager was VERY helpful for optimizing and customizing Logos4 for Catholic users. Use of Collections is a must so you can restrict your research to Catholic resources only. Also, customizing the Passage Search is also mandatory, that is unless you want Protestant audio sermons or PowerPoint sermon presentations returned in your searches. (Note, you will invariably find these in error. However, these Protestant resources serve a dual purpose: to learn just what some Protestants believe (each acting as his own Pope) and for, well, humor gained from the interesting mental gymnastics Protestants go through to keep from taking a cccccccatholic position on anything.
From a practical point of view, the more Catholics that use Logos4 and request Catholic resources, the more the Truth will get out there. Heck, a Protestant or two might very well look at the wonderful treasure of the Church and be “convicted.”
In short, I think Logos4 is a very, very powerful program. I would be hesitant, however, to recommend it to anyone not strong in their faith. It is a research tool first and foremost; unless you restrict yourself to Catholic resources only, you will need to discern, discern, discern.