Maybe it's easier to first think about MaxSpec of a (commutative) ring R. This is the set whose points are the maximal ideals of R. How does this come up? Well, think back to affine varieties, say over \mathbb{C}. The main idea of algebraic geometry is, of course, to translate geometry into algebra and vice versa. The first thing you probably learn in this vein is that to each variety V \subset \mathbb{C}^n we can associate a ring \mathbb{C}[V]--the coordinate ring of V--which we can use in our geometry-algebra dictionary. Then you learn that, by the Nullstellensatz, the maximal ideals of \mathbb{C}[V] are in 1-1 correspondence with points in V. In other words, the sets \text{MaxSpec}\mathbb{C}[V] and V are pretty much the same. And we can say a bit more: the Zariski topology (which is just a fancy way of keeping track of sub-geometric objects--or subvarieties--of V) induces a topology on \text{MaxSpec}\mathbb{C}[V]. This is done as follows. A subvariety U of V gives us an ideal I(U) containing the ideal I(V), and so U corresponds to the maximal ideals of \mathbb{C}[V]=\mathbb{C}[x_1,\ldots,x_n]/I(V) that contain I(U). So we say that a subset of \text{MaxSpec}\mathbb{C}[V] is (Zariski-)closed if it consists entirely of maximal ideals of \mathbb{C}[V] which contain a given ideal of \mathbb{C}[V], and you can check that this indeed generates a topology.
Now, given an arbitrary ring R, we can look at its MaxSpec and give it this type of Zariski topology. And then we try to see how far MaxSpecR behaves as a MaxSpec of a coordinate ring of a variety. And then one notices that using prime ideals instead of maximal ideals has some "benefits."
Finally, as to your other question about a relation to the spectrum "in" Fourier transform, then this depends on what you mean by "spectrum." Personally I've never seen a definition for the spectrum of the transform itself. However, the transform on say the commutative Banach algebras L^1(\mathbb{R}) or L^1(S^1) (or indeed on any L^1 of a locally compact abelian group G) is nothing other than the Gelfand transform of these Banach algebras -- something very closely related to the "spectrum" of the algebras. The spectrum specA of commutative Banach algebra A is defined to be the set of maximal ideals of A--surprise, surprise! (Well, not quite. We actually need maximal "modular" ideals: a (closed) ideal I of A is said to be modular if the algebra A/I is unital. If memory serves me, I think for A=L^1 all the maximal ideals are modular, but I could very well be wrong.) One can put a topology on specA and then one has a theorem that gives a map (called the Gelfand transform) A \to C_0(\text{spec}A), where C_0 is the space of continuous functions vanishing at infinity. For the case of A=L^1(R) or L^1(S^1), one can prove that specA=R or Z, respectively, and then one sees that the Gelfand transform in this case is the Fourier transform.