SODOM & GOMORRAH: Does John Locke's call for religious toleration display an immense intolerance toward religion?
The fact that anyone in our secular age would ask the question already reveals the answer the questioner has in mind: yes. A normal, modern reading of John Locke's A Letter Concerning Toleration would fill the typical person's heart with warmness and joy; an unfiltered, heretical reading leaves a person horrified at Locke's complete fumbling of theological issues, his arrogant disdain for serious belief, and his inability to follow an argument to its conclusion. If this is John Locke's religious toleration, we should be very concerned.
John Locke's A Letter Concerning Toleration forms the basis of the liberal (classical and modern) argument today: religion is a matter of personal opinion and should therefore be expressed only in the private sphere. In order to make this argument, we would contest that John Locke must relativize and trivialize religious ceremony to be “mere opinion” and silly in order to justify its exclusion from public life.
Locke, hardly the master of subtlety, starts his letter of intoleration with a broad attack on all serious religion. He writes, “I esteem that Toleration to be the chief Characteristical Mark of the True Church […] everyone is Orthodox to himself.” 
This is a double pronged attack. First, Locke has labeled all those who would disagree with his letter as being excluded from the Body of Christ (which makes up the True Church). He has second, informed us that orthodoxy stems from individual adherence to individual belief. It does not, as was asserted by churches at the time, come from the authority of priests, and it does not, as asserted by this author, stem from God. It comes from the individual.
Toleration for Locke means that the churches must stand down. He tells us that churches have no “Jurisdiction in Worldly matters”, which means simply that religion has no weight on what people actually do. Instead, we must find our own paths.  Locke says that “in this great variety of ways that men follow, it is still doubted which is the right one.”  He takes direct issue with Christ's proclamation that He is the Way; Locke does not seem quite sure which way is the Way, or at the least because those who do not follow Christ dispute His claim to be the Way, Locke doesn't feel comfortable in informing them of their error. The Way is either unknown, not the Way, or not worth being discussed. This begins John Locke's efforts at relativizing and trivializing Christian tradition.
Once he has completed his assault on the Way, John Locke's religious toleration attacks baptism and holy communion. First, he states that no one would ever get upset about how one washed an infant, but plenty of people get upset about how baptism is carried out when sprinkling water is an indifferent activity. Second, he says that no one would become angry over eating bread and drinking wine, but people take offense at allowing or disallowing others to take communion when eating and drinking are indifferent things. Locke claims that these have been relegated to “human discretion” precisely because they're indifferent.
Locke on religion is a Locke who has trivialized religious ceremony by relativizing everything that caused contention in his time. If he made baptism, communion, and critical scriptural differences to be matters of indifference, people would stop fighting about them and Locke could lay claim that his tolerance (read as: watered down, sanitized faith) would create “peace and security.” Locke and his secular followers miss a few critical points.
First, baptism, communion, and scripture aren't matters of indifference. To say that they don't matter is just as strong a statement about them as saying that they do. Second, any statement about religion's role in public affairs is both a religious and political statement. It is a statement about faith's power or lack of power in our lives and it's a statement about what counts and doesn't count in politics. Locke kids himself when he claims that decisions in one realm don't or shouldn't impact the other: being told you don't have a voice is one of the largest impacting decisions that can be made. Third, Locke's letter concerning religious toleration only attains their peace and security by stripping the value out of belief. We may agree that wars, deprivation of liberty, and so forth, in the name of religion are harmful and tragic, but we can also agree that what's worth living for is also worth dying for and taking that away is also positively tragic.
Citactions from Locke, John. A Letter Concerning Toleration. Indianapolis, Indiana: Hackett Publishing Company. 1983.
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