Warning: incoming eyesore.
Introduction
Using the binomial theorem,
\begin{align*}
\int_{0}^{1} \frac{x^n (1 - x)^n}{1 + x^2}\,\text{d}x &= \int_{0}^{1} \frac{x^n}{1+x^2}\sum_{m = 0}^{n} {n \choose m}(-1)^{m}x^m\,\text{d}x \\
&= \sum_{m = 0}^{n} {n \choose m}(-1)^{m} \int_{0}^{1} \frac{x^{n+m}}{1+x^2} \,\text{d}x
\end{align*}
Suppose first that $n + m = 2q$ for some $q$ then
$$
\frac{x^{2q}}{1+x^2} = \frac{(-1)^{q}}{1 + x^2} - \sum_{\ell = 0}^{q - 1}(-1)^{\ell + q}x^{2\ell}
$$
Therefore,
$$
\int_{0}^{1} \frac{x^{2q}}{1+x^2} = (-1)^{q}\frac{\pi}{4} - \sum_{\ell = 0}^{q - 1} \frac{(-1)^{\ell + q}}{2\ell + 1}
$$
Now suppose that $n + m = 2p + 1$ for some $p$ then
$$
\frac{x^{2p + 1}}{1+x^2} = \frac{(-1)^{p}x}{1 + x^2} - \sum_{\ell = 0}^{p - 1}(-1)^{\ell + p}x^{2\ell + 1}
$$
Therefore,
$$
\int_{0}^{1} \frac{x^{2p + 1}}{1+x^2} \,\text{d}x =\frac{(-1)^{p}}{2}\ln(2) - \sum_{\ell = 0}^{p - 1} \frac{(-1)^{\ell + p}}{2\ell + 2}
$$
Case: $n$ even
If $n$ is even then write $n = 2n'$ and then
\begin{align*}
\int_{0}^{1} \frac{x^{2n'} (1 - x)^{2n'}}{1 + x^2}\,\text{d}x &= \sum_{m = 0}^{2n'} {2n' \choose m}(-1)^{m} \int_{0}^{1} \frac{x^{2n'+m}}{1+x^2} \,\text{d}x \\
&= \sum_{m = 0}^{n'} {2n' \choose 2m} \int_{0}^{1} \frac{x^{2(n'+m)}}{1+x^2} \,\text{d}x \\
&- \sum_{m = 0}^{n' - 1} {2n' \choose 2m + 1} \int_{0}^{1} \frac{x^{2(n'+m) + 1}}{1+x^2} \,\text{d}x
\end{align*}
Use the previous results
\begin{align*}
\int_{0}^{1} \frac{x^{2n'} (1 - x)^{2n'}}{1 + x^2}\,\text{d}x &= \sum_{m = 0}^{n'} {2n' \choose 2m}\left[(-1)^{n' + m}\frac{\pi}{4} - \sum_{\ell = 0}^{n' + m - 1} \frac{(-1)^{\ell + n' + m}}{2\ell + 1} \right] \\
&- \sum_{m = 0}^{n' - 1} {2n' \choose 2m + 1} \left[ \frac{(-1)^{n' + m}}{2}\ln(2) - \sum_{\ell = 0}^{n' + m - 1} \frac{(-1)^{\ell + n' + m}}{2\ell + 2} \right]
\end{align*}
Case: $n$ odd
If $n$ is odd then write $n = 2n' + 1$ and then
\begin{align*}
\int_{0}^{1} \frac{x^{2n' + 1} (1 - x)^{2n' + 1}}{1 + x^2}\,\text{d}x &= \sum_{m = 0}^{2n' + 1} {2n' + 1 \choose m}(-1)^{m} \int_{0}^{1} \frac{x^{2n'+m + 1}}{1+x^2} \,\text{d}x \\
&= \sum_{m = 0}^{n'} {2n' + 1\choose 2m} \int_{0}^{1} \frac{x^{2(n'+m) + 1}}{1+x^2} \,\text{d}x \\
&- \sum_{m = 0}^{n'} {2n' + 1 \choose 2m + 1} \int_{0}^{1} \frac{x^{2(n'+m + 1)}}{1+x^2} \,\text{d}x
\end{align*}
Again, using the previous results,
\begin{align*}
\int_{0}^{1} \frac{x^{2n' + 1} (1 - x)^{2n' + 1}}{1 + x^2}\,\text{d}x &= \sum_{m = 0}^{n'} {2n' + 1 \choose 2m}\left[\frac{(-1)^{n' + m}}{2}\ln(2) - \sum_{\ell = 0}^{n' + m - 1} \frac{(-1)^{\ell + n' + m}}{2\ell + 2} \right] \\
&- \sum_{m = 0}^{n' - 1} {2n' + 1 \choose 2m + 1} \left[ (-1)^{n' + m + 1}\frac{\pi}{4} - \sum_{\ell = 0}^{n' + m} \frac{(-1)^{\ell + n' + m + 1}}{2\ell + 1} \right]
\end{align*}
Those sums are all finite, so in principle that's the solution. I can't immediately see how to simplify it though.