Let
$$
H=\left(
\begin{array}{cc}
-1 & 1 \\
1 & -1 \\
\end{array}
\right) \tag{1}
$$
Then the continuous transformation
$$
U(t)=e^{i t H}=
\left(
\begin{array}{cc}
\frac{1}{2} \left(1+e^{-2 i t}\right) & \frac{1}{2}-\frac{1}{2} e^{-2 i t} \\
\frac{1}{2}-\frac{1}{2} e^{-2 i t} & \frac{1}{2} \left(1+e^{-2 i t}\right) \\
\end{array}
\right)
$$
gives $$
U(\pi/2)=\left(
\begin{array}{cc}
0 & 1 \\
1 & 0 \\
\end{array}
\right)\, . \tag{2}
$$
$H$ "generates" a one-parameter group of unitaries $U(t)$ because
$U(t)$ is constructed using powers $\hat H$, in the same way that a finite group is generated by taking powers of its generating elements (although here you're also adding powers of $H$, something you can't do for elements of a finite group). Here, $U(t)$ happens to coincide with your transformation at $t=\pi/2$.
Since the elements of the unitary $U(t)$ can be complex and do not sum to $1$ along lines or columns, it does not really the probabilities directly; the probabilities are actually moduli squared (thus real) of projections: these moduli squared, when summed along a line or a column, do sum to $+1$.
In the reverse direction, given a unitary $U$ is it not directly possible to obtain $H$ without some tinkering. Whereas
$$
\frac{dU}{dt}\vert_{t=0}=iH
$$
would allow you to recover $H$, you can't really take the derivative of Eq.(2) no more than it makes sense to take the derivative of a function evaluated at one point. One way to find Eq.(1) is to write the most general $2\times 2$ Hermitian matrix (which would depend on $4$ real parameters), take its exponential and select the parameters to give you (2). This isn't so bad for $2\times 2$ matrices but it can become quite complicated for larger matrices.
A more systematic way starts with
$$
U=\left(\begin{array}{cc} 0 & 1 \\ 1 &0\end{array}\right)
$$
and write
$$
U=\left(
\begin{array}{cc}
-\frac{1}{\sqrt{2}} & \frac{1}{\sqrt{2}} \\
\frac{1}{\sqrt{2}} & \frac{1}{\sqrt{2}} \\
\end{array}
\right)\,\left(\begin{array}{cc}
-1&0\\
0&1\end{array}\right)
\left(
\begin{array}{cc}
-\frac{1}{\sqrt{2}} & \frac{1}{\sqrt{2}} \\
\frac{1}{\sqrt{2}} & \frac{1}{\sqrt{2}} \\
\end{array}
\right)
$$
and find
$$
u(t)=\left(\begin{array}{cc}
e^{-i k_1 t}&0\\
0&e^{ik_2t}\end{array}\right)
$$
so that
$$
u(t_0)=\left(\begin{array}{cc}
-1&0\\
0&1\end{array}\right)
$$
Thus for instance, take $t_0=\pi/2 $ (as before) to get $k_1=2, k_2=4$
and then
$$
H=\left(
\begin{array}{cc}
3 & 1 \\
1 & 3 \\
\end{array}
\right)\, . \tag{3}
$$
You can then verify that $e^{i pi H/2}=U$. If anything, this show that $H$ is not unique: in fact this $H$ of Eq(3) different from $H$ of Eq(1) by a multiple of the unit matrix. (The choice $k_2=0$ gives $H$ in Eq.(1).) Moreover, choosing different $t_0$ will produce different $H$'s.