A fun problem. I think that the following approach is natural (at least it is the first that occurred to me, YMMV).
Let us consider the union
$$
A=\bigcup_{i=1}^nA_i.
$$
I will work in the space $F_A$ of real valued functions from $A$ to $\mathbb{R}$.
If you list the elements of $A$ like
$$
A=\{a_1,a_2,\ldots,a_m\},
$$
you can identify the space $F_A$ with vectors of $\mathbb{R}^m$. The identification is natural. We identify the function $f:A\to\mathbb{R}$ with the vector
$$
\vec{f}=(f(a_1),f(a_2),\ldots, f(a_m))\in\mathbb{R}^m.
$$
Let us denote by $\chi_i$ the characteristic function of the subset $A_i$, that is the function in $F_A$ defined by $\chi_i(a)=1$, if $a\in A_i$, and $\chi_i(a)=0$, if $a\notin A_i$.
Let $x_i,i=1,2,\ldots,n$ be arbitrary real numbers as in your question. Consider the function
$$
f=\sum_{i=1}^n x_i\chi_i\in F_A.
$$
Let us look at the vector $\vec{f}\in\mathbb{R}^m$. I denote by $\langle\ ,\ \rangle$ the usual inner product of the space $\mathbb{R}^m$. We have trivially
$$
\langle \vec{f},\vec{f}\rangle=\Vert\vec{f}\Vert^2\ge0.
$$
On the other hand we have
$$
\vec{f}=\sum_{i=1}^n x_i\vec{\chi_i}.
$$
Bilinearity of the inner product gives us thus that
$$
\langle\vec{f},\vec{f}\rangle=\sum_{i=1}^n\sum_{j=1}^n x_i x_j\langle\vec{\chi_i},\vec{\chi_j}\rangle.
$$
But, more or less obviously (think about the inner product of two distinct vectors both with components zero or one only), we also have
$$
\langle\vec{\chi_i},\vec{\chi_j}\rangle=|A_i\cap A_j|=a_{ij}.
$$
The claim about non-negativity follows from this.