The reason why we can use the Fourier transform to solve differential equations is because the following diagram commutes (from the same Wikipedia article):

The commutative diagram is simply a reasoning device that helps clarify the relationship between certain processes/functions. Often, the fact that a diagram commutes means we can express the same result in two (or more) ways.
Each of these ways might have its own advantages or disadvantages, but knowing that they give the same result (i.e. the diagram commutes) gives us the freedom to choose the method that best suits our purposes.
In simple cases (like the Fourier transform), a commutative diagram probably just tells us something we already know. However, in more complex systems/situations, drawing a commutative diagram might help you see/make use of/make sense of relationships that you might have otherwise missed.