Let's understand this from the point of view that pions are pseudogoldstone bosons.
Suppose for case of $SU_{L}(2)\times SU_{R}(2)$ we have bilinear form
$$
\tag 0 L_{qq} = \bar{q}_{i}q_{i}, \quad i = u, d
$$
As we know, below $\Lambda_{QCD}$ scale spontaneously breaking symmetry group down to diagonal group $SU_{V}(2)$ arises. By using the usual technique we may extract goldstone degress of freedom from quark fields,
$$
q_{i} \equiv (U\tilde{q})_{i}, \quad U \equiv \text{exp}\left[ i\gamma_{5}\frac{\epsilon_{a}t_{a}}{f_{\pi}}\right],
$$
where $t_{a}$ are Pauli matrices and $\epsilon_{a}$ are real-valued coordinate dependent parameters, ans then replace bilinear forms to VEVs:
$$
\tag 1 \bar{\tilde{q}}_{i}\tilde{q}_{j} \to V\delta_{ij}, \quad \bar{\tilde{q}}_{i}\gamma_{5}\tilde{q}_{j} \to 0
$$
Note that $\epsilon_{a}t_{a}$ may be parametrized, by using explicit form of Pauli matrices, in a form
$$
\tag 2 \epsilon_{a}t_{a} = \begin{pmatrix} \frac{\pi^{0}}{\sqrt{2}} & \pi^{-} \\ \pi^{+} & -\frac{\pi^{0}}{\sqrt{2}}\end{pmatrix},
$$
where $\pi^{\pm} \equiv \epsilon_{1} \pm i\epsilon_{2}$. As we see, we explicitly obtain one neutral degree of freedom, $\pi^{0}$, and two charged, $\pi^{\pm}$. Now let's calculate one-pion transition amplitude from $(0)$,
$$
\langle 0 | \bar{q}_{i}q_{i}|\pi^{0}\rangle,
$$
by using $(1)$ and $(2)$. We immediately obtain that
$$
\langle 0 | \bar{q}_{i}q_{i}|\pi^{0}\rangle \equiv \frac{i}{\sqrt{2}f_{\pi}}\langle 0|\bar{\tilde{q}}_{i}t_{3}^{ij}\tilde{q}_{j}\pi^{0}|\pi^{0}\rangle \simeq \frac{i}{\sqrt{2}f_{\pi}}\langle 0|\bar{\tilde{u}}\tilde{u}-\bar{\tilde{d}}d|0\rangle,
$$
which immediately gives statement that the pion is combination of $uu, dd$ with the minus sign because of it is the parametrization of goldstone degree of freedom in case of broken $SU_{L}(2)\times SU_{R}(2)$ group, not $U_{L}(2)\times U_{R}(2)$. The combination with the "plus" sign corresponds to parametrization of $U(1)$ group. As you know, this is $\eta$ meson for $SU_{L}(2)\times SU_{R}(2)$ group and $\eta{'}$ meson for $SU_{L}(3)\times SU_{R}(3)$ group. Of course, these combinations appear in nature.