A lot of the time people will use the term breaking out of the matrix. As if that is a good thing I have used it too in the past. However, if one realizes the Matrix Universe of fiction comes from an antichrist Gnostic worldview one should not be associating themselves with these ideas.
The Matrix takes the truth of God being one of absolutes and order as the enemy. Otherwords it's against God Himself whom is a God of Order. It also paints a view of the world that is equally unbiblical. Saying that God is not in charge of whom gets into power or taken out of power, but, instead Evil entities. When the Biblical view is that God is Sovereign over everything including the authorities.
The One Worlders and Mystery Babylon are not Sovereign and in charge of all that comes to pass. That is God and God alone. The Bible calls satan as the little g god of this age and not god of this world as some believe. The Word used in Greek is aeon or age not cosmos.
The Matrix motif also makes one question God's Creation by bringing in the idea of an illusion based reality. Instead of being able to actually study and understand the Creation without assuming you cannot trust your senses. The science of Creation is something you can study and come to Biblical conclusions on without saying all science is a lie. Being against scientism is not the same thing as saying science itself is a lie.
Taking a pill to have more knowledge is also a motif coming from lucifar and the Garden of Eden. It is the idea of "enlightenment." This is not a Godly thing, but, an antirchrist thing. The very core of the ideology behind the series is antichrist Gnostic teaching. No one should be referencing it as a good place to get inspiration from.
It also pushes an unbiblical view of outright rebellion instead of peaceful attempts to change things for the better. As Christians we know that only certain types of resistance are Biblical and outright rebellion is not one of them. We need to always keep in mind that all authorities are setup and torn down by God Himself. Therefore, our resistance is peaceful and not based on overthrowing authorities setup by God. We want the authorities to acknowledge and follow God's Law Word not be overthrown. This is the purpose of the docterine of lesser magistrates.
The something can be said of any number of institutions that exist. Wanting a change in the health care system does not mean we live in outright rebellion against all forms of medicine for example.