Well, objects without morphisms are essentially boring. Think of finite-dimensional vector spaces over a field $K$. They are all essentially just $K^n$. So why study them at all? Well, the linear maps between them are interesting! One would like to classify them.
Morphisms serve as "communication" between objects. The theme "arrows are more important than objects" is best illustrated in full generality by the Yoneda Lemma. But actually there are a lot of familiar and specific examples in mathematics.
Algebra: The fundamental theorem on homomorphisms is the tool to work with quotient groups (as well as quotient rings, etc.). It is not really important that they are made up out of cosets, but rather that homomorphisms $G/N \to H$ correspond to homomorphisms $G \to H$ which "kill" $N$. Actually this is the whole idea of this construction: We want to kill elements.
Algebraic geometry: Let $f \in \mathbb{Z}[x,y]$ be a polynomial in two variables, for example $f(x,y) = x^2 - 2 y^2$. Then the solutions of $f$ in a commutative ring $R$ are exactly the homomorphisms of rings $\mathbb{Z}[x,y]/(f) \to R$.
Differential geometry: One tries to understand a manifold $M$ by means of its vector bundles, which are maps $V \to M$ (with extra structure).
Algebraic topology: One tries to understand a nice space $X$ by means of its homotopy groups, which are made up out of maps $S^n \to X$ in the homotopy category. These are groups because $S^n$ carries a natural cogroup structure.
Combinatorics: A coloring of a set $X$ with $n$ colors is just a map $X \to \{1,2,\dotsc,n\}$.
Representation theory: We try to understand a group $G$ by its $K$-linear representations, which are homomorphisms $G \to \mathrm{GL}_n(K)$.
The list is endless, therefore I will stop here. It is very easy to find examples, because almost every modern mathematical publication promotes the theme.
You might be also interested in the theme of "categorical characterizations", started by Freyd, Bergman and others (see for instance here or there or here).