I just realized that I can do a similar proof with the countably infinite set of pairs of rationals!
Let $C$ be the set of all pairs of nonnegative rationals $(x,y)$ such that $x<y$. For each particular $(x,y) \in C$ we have (by the same argument I give in the question itself):
\begin{align}
P[X(x) \leq X(y)] &= P[X(y)-X(x)\geq 0] \\
&\overset{(a)}{=} P[X(y-x)-X(0)\geq 0] \\
&\overset{(b)}{=} P[X(y-x)\geq 0] \\
&= 1
\end{align}
where (a) holds by the stationary increment property; (b) holds because $X(0)=0$ with probability 1.
Thus, because $C$ is a countably infinite set, we have:
$$ P[\cap_{(x,y)\in C} \{X(x)\leq X(y)\}] = 1$$
That is, with probability 1, the sample path $X(t)$ has no instance of rationals $x,y$ such that $0\leq x<y$ and $X(x)>X(y)$.
Edit 1 : Additionally assuming right-continuity
Now suppose that The Levy process is also required to be right-continuous everywhere (definitions of Levy processes vary, this is not on the 4 properties of the wikipedia link but it is in other definitions):
Assuming right-continuity, if there are times $u,v$ such that $0\leq u<v<\infty$ and $X(u)>X(v)$, it would mean that there are rational numbers $u+\epsilon$ and $v+\delta$ (with $\epsilon\geq 0, \delta\geq 0$) such that $u+\epsilon < v+\delta$ and $X(u+\epsilon)>X(v+\delta)$. But we already know that existence of any two rational numbers $x<y$ for which $X(x)>X(y)$ is an event that has probability 0.
So, indeed, if the Levy process is nonnegative with probability 1, and if it is also required to be right-continuous everywhere, then it is also nondecreasing with probability 1.
Edit 2: Counter-example
Here is an example process $X(t)$ that satisfies the 4 properties on wikipedia, is surely nonnegative, but is surely not right continuous, and with positive probability it is not nondecreasing:
For $t\geq 0$, let $N(t)$ count the number of arrivals in a Poisson process with rate $\lambda=1$. Notice that $N(t)$ surely takes integer values. (Perhaps it is better to say that $N(t)$ "almost surely" takes integer values if we are worried about the possibility of an infinite number of arrivals in finite time. Of course, we can remove all such instances from the sample space without affecting distributions, and if we view $N(t)$ as the result of such a "trimmed" sample space then we get back the ability to say "surely").
Let $U$ be an independent random variable that is uniform over $(0,1)$. For $t\geq 0$ define
$$Z(t) = \left\{ \begin{array}{ll}
0 &\mbox{ if $t\neq U$} \\
77.5 & \mbox{ if $t=U$}
\end{array}
\right.$$
Define $X(t) = N(t)+Z(t)$. It is easy to see that $X(t)$ satisfies the 4 properties on wikipedia because: $X(0)=0$ almost surely; $X(t)$ has stationary and independent increments (indeed, given any finite or countably infinite list of (deterministic) times $\{t_1, t_2, t_3, ...\}$, with probability 1 $U$ does not lie on those times hence the $Z(t)$ process does not affect increments during those times); it has the "continuity in probability" property.
But $X(t)$ is not right-continuous: Surely, $X(t)$ is integer-valued for all $t \neq U$, while $X(U)=N(U)+77.5$, which is not an integer. So, surely, $X(t)$ is not right-continuous at $t=U$ (a sequence of integers cannot converge to the noninteger value $N(U)+77.5$).
And $X(t)$ is not nondecreasing: We show that $P[X(U)>X(U+1)]>0$ and so with positive probability the sample path $X(t)$ is not nondecreasing:
\begin{align}
P[X(U)> X(U+1)] &=P[77.5+N(U)>0+N(U+1)] \\
&\overset{(a)}{\geq} P[77.5 > N(U+1)]\\
&\overset{(b)}{\geq} P[77.5 > N(2)]\\
&>0
\end{align}
where (a) holds because $N(U)\geq 0$ surely; (b) holds because $N(t)$ is surely nondecreasing and $U+1\leq 2$ so $N(U+1)\leq N(2)$.