There are several elementary points that can be made :
- On the other hand, why consider only homology ? I don't see why one would be more natural than the other (actually for me cohomology seems more natural because I'm used to subjects where cohomology natuarally appears).
- There are cohomology theories that are clearly useful and natural and are related to singular cohomology : de Rham cohomology, group cohomology and Galois cohomology, sheaf cohomology for instance. They often appear when you are interested in deriving a left exact functor and not a right exact one, which... happens.
- There are duality theorems (all kind of variants of Poincaré duality) that make use of cohomology, so even if ultimately you are interested in homology, studying cohomology can be useful.
- Cohomology natually carries a sort of algebra structure given by the cup product, which is really helpful in a lot of situations.
I'll give an explicit example coming from algebra since this is what I understand best. Take $G$ a finite group, and $X = K(G,1)$ the corresponding Eilenberg-MacLane space (so $\pi_1(X)=G$ and $\pi_i(X)=0$ if $i>1$). Then you can write $H_n(G,A) := H_n(X,A)$ and $H^n(G,A):= H^n(X,A)$ for any abelian group $A$.
This is a special case of group homology/cohomology (namely the case where $G$ acts trivially on $A$). And though group homology is quite useful (for instance Hurewitz's theorem says that $H_1(G,\mathbb{Z}) = G^{ab}$), group cohomology appears way more often, so singular cohomology in this context is more useful.
Now if you don't care about groups you may not be happy with that, but even if you're only interested in topology, clearly $X = K(G,1)$ is an interesting space since it's "the space that only has $\pi_1(X) = G$ in its homotopy". So understanding maps $Y\to X$ is clearly a natural question.
And if $G$ is abelian you have the result that for any CW-complex $Y$, $[Y,K(G,n)] \simeq H^n(Y,G)$, so singular cohomology (with coefficients) classifies maps to Elenberg-MacLane spaces (up to homotopy).