- A topological space is nothing more or nothing less than its definition, which is based upon open sets.
This being said, topological spaces bear the same relation with classical $\mathbb{R}^2$ and $\mathbb{R}^3$ geometry, as, let's say, groups with arithmetics: that's the cradle of the concept. But like any math concept, it is born to leave its cradle and explore remote places. Like groups are omnipresent in maths, topological spaces are everywhere. For example there is a demonstration of the infinitude of prime numbers, that uses a specific topology on $\mathbb{N}$.
Saying that topology is about "sets of points that are arranged in a certain way geometrically (like a line, shape, plane)" is somewhat misleading: notions of line and plane require a vector space and usually imply a metric; topology is more general than that. Topology allows to extend important notions such as function continuity, to spaces that, e.g., do not have any metric. Such as the vector space of functions from $\mathbb{R}$ to $\mathbb{R}$ with pointwise convergence topology: it cannot be given a metric that preserves its topology.
As an example, Zarisky topologies are defined by their closed sets, which are algebraic varieties (solutions of a system of polynomial equations). We may still be in $\mathbb{R}^n$ or $\mathbb{C}^n$, so it can still be visualized, but the closed sets are different from those of standard topology on those spaces.
Strictly speaking, "continuous deformations" refer to homotopies, not homeomorphisms. Homotopy is defined between functions; then a derived concept, homotopy equivalence (or homotopy types) is defined between sets.
Homeomorphism is actually a stronger property than homotopy equivalence; i.e. you can have two spaces that are homotopy equivalent, but not homeomorphic, but homeomorphism implies homotopy equivalence.
- Topology deals with properties of space that do not require a distance. It does that by specifying "open sets". While their definition sounds abstract, you can actually easily express notions such as separation with them. There are actually many different concepts of separation. The most commonly used is: two points are separated if you can find two open sets, each open set contains one of these points, and their intersection is empty.
A space is connected if it cannot be partitioned into two disjoint non-empty open sets. This is tricky because openness is not an absolute, but a relative notion, and here the subsets are considered open relatively to their superset. E.g. $S = [0, 1] \cup [2, 3]$ is disconnected because it is the union of $[0, 1]$ and $[2, 3]$, which are both open subsets of S. (And they are also closed subsets of S and of $\mathbb{R}$, of course).
Like for separation, there are various non-equivalent concepts for connectedness.
- Assuming you mean the tiling with edges and vertices, not with full-surface hexagons. Then you could define open sets by all open-ended connected paths between any two points of the tiling, and their unions. That would be equivalent to the restriction of open sets of the plane, to the tiling.
Another possibility, more specific to the tiling, would be to define closed sets as edges, and finite sets of edges. Open sets being the complementary sets. That would mean two points in the same edge (that are not vertices) would not be separated. Which is adequate if we think of the tiling primarily as a graph.