I can't prove it either, but I have a framework where this result fits. If you write the sum as $$S_n = \sum_{i,j=1}^n \frac1{2i+1}\frac1{2j+1} \frac{(-1)^{i+j}(n+1)^2}{i+j}{n\choose i}{n+i\choose i-1} {n\choose j}{n+i\choose j-1}$$ and use the fact that $${n+i\choose i} = \frac{n+1}i{n+i\choose i-1}$$, you see that $$S_n = \sum_{i,j=1}^n \frac1{2i+1}\frac1{2j+1} \frac{(-1)^{i+j}ij}{i+j}{n\choose i}{n+i\choose i} {n\choose j}{n+i\choose j}.$$ That sum looks remarkably similar to those that occurred in http://mathhelpboards.com/linear-abstract-algebra-14/find-a_1-3-a_2-5-a-7056.html (see in particular the equations labelled (1) and (2) in my comment #4 there). Using the notation of that thread, let $H_n$ be the $n\times n$ Hilbert matrix, let $H_n^{-1} = X_n^*X_n$ be the factorisation of its inverse into lower- and upper-triangular matrices, and let $k$ be the vector $\bigl(\frac13,\frac15,\ldots, \frac1{2n+1}\bigr).$ Then your sum $S_n$ is exactly one-quarter of the sum in that other thread, namely $S_n = \langle H_n^{-1}k,k\rangle = \|X_nk\|^2$. In that thread, anemone and I decided that this must be equal to $\frac14\!\bigl(1-\frac1{(2n+1)^2}\bigr)$, which agrees with your conjecture $S_n = \frac{n(n+1)}{(2n+1)^2}.$ But I still can't prove it!