This is rooted in the fact that "true" and "provable from a certain set of axioms with a legit sequence of deductions" can be different things, and in most cases a direct proof can be easier to generalize than an indirect proof. A couple of examples might be useful in explaining this.
Theorem. If the elements of $\mathbb{N}$ are colored with $c$ colors, there are infinite monochromatic 3-APs (arithmetic progressions with $3$ terms).
Sketch of indirect proof: we may invoke the https://en.wikipedia.org/wiki/Poincaré_recurrence_theorem and the principle of combinatorial compactness, by putting a tolopogy over the space of ultrafilters.
Sketch of direct proof: we may study the discrete Fourier series of the set of integers with some color. It turns out that if a coefficient is large enough, there is no way to avoid monochromatic $3$-APs. If that is not the case, we are able to achieve an increase in density by intersecting our set with an infinite AP. By dichotomy, a finite number of steps (only depending on $c$) is able to locate a monochromatic $3$-AP, and prove it appears before $\exp(\exp(\exp c)))$ or something like that.
The indirect case might be considered more elegant, but the direct proof provides an extra quantitative information.
Theorem. Any continuous map $f$ from the unit disk to itself has a fixed point.
Sketch of indirect proof: the existence of a continuous map from $D^2$ to $D^2$ without fixed points would give a retraction of $D^2$ over $S^1$, which does not exist due to the fact that $\pi_1(D^2)$ is trivial while $\pi_1(S^1)=\mathbb{Z}$.
Sketch of direct proof: $D^2$ can be continuously deformed into a triangle $T$, and we may consider a triangulation of $T$ with mesh $\varepsilon$. We may assign a color to each vertex of the triangulation according to the value of our function at such point, and check that the hypothesis of Sperner's lemma are fulfilled. The full-colored Sperner's triangles associated to the meshes $\frac{\varepsilon}{2},\frac{\varepsilon}{4},\frac{\varepsilon}{8},\frac{\varepsilon}{16},\ldots$ accumulate towards a fixed point for $f$.
The (combinatorial) direct proof not only proves a fixed point exists, it provides an algorithm for locating it.