The answer is no. Take for instance $d = 2, m = 5, r = 4$. More generally, for any $d$, you can find infinitely many values $m$, for which at least $d-1$ values $r$ with $0 \le r < m$ have no solution to $\binom{x}{d} \equiv r \pmod m$. More details follow.
For $d = 0$, the answer is trivially no: $f(x) = \binom{x}{0} = 1$ for all $x$, so we can't have a solution to $f(x) \equiv r \pmod m$ when $r \not\equiv 1 \pmod m$.
For $d=1$, the answer is trivially yes: $f(x) = \binom{x}{1} = x$ for all $x$, so for any $(r,m)$, one solution to $f(x) \equiv r \pmod m$ is to take $x = r$.
For $d\ge 2$ is when it gets interesting. Let's start with $d = 2$. Then $f(x) = \binom{x}{2} = \frac{x(x-1)}{2}$, and we want to know whether the equation $f(x) \equiv r \pmod m$ always has a solution for any $(r,m)$. Looking at the sequence of values $f(x)$, this is OEIS A161680. If you look at its sequence of last digits (corresponding to $m = 10$), you see (this is more convenient if you view it as a list) that it is periodic with period $20$, and the only last digits that appear are ${0, 1, 3, 5, 6}$. The other digits ${2, 4, 7, 8, 9}$ never appear. In fact this is easy to prove: for $x \equiv y \pmod {20}$, we have $x(x-1) \equiv y(y-1) \pmod {20}$ which is equivalent to $\dfrac{x(x-1) - y(y-1)}{20}$ being an integer, and thus to $\dfrac{\frac{x(x-1)}2 - \frac{y(y-1)}{2}}{10}$ being an integer, which means that $\frac{x(x-1)}{2} \equiv \frac{y(y-1)}{2} \pmod {10}$. So the sequence is indeed periodic with period $20$. And after this it's just a matter of inspection to see that the only last digits that do occur are as above.
In general, by the same reasoning, the sequence $\binom{x}{2} \bmod m$ has $2m$ as a period. (In other words, $x \equiv y \pmod {2m} \implies \binom{x}{2} \equiv \binom{y}{2} \pmod m$.) In particular, taking $m = 5$, we note that the sequence $\binom{x}{2}$ goes as $0, 0, 1, 3, 1, 0, 0, 1, 3, 0, 0\dots$ so it's in fact periodic with period $5$, and the remainders $2$ and $4$ never occur.
Edit: Even more generally, whenever $\gcd(m, d!) = 1$, the sequence $\binom{x}{d} \bmod m$ has $m$ as a period. Proof: if $x \equiv y \pmod m$, then $x-k \equiv y-k \pmod m$ for all $k$, so
$$x(x-1)(x-2)\dots(x-d+1) \equiv y(y-1)(y-2)\dots(y-d+1) \pmod m$$
Now as $\gcd(d!, m) = 1$, we can "divide" both sides by $d$. More accurately, $d$ has an inverse modulo $m$, i.e. a number $d'$ such $dd' \equiv 1 \pmod m$, so multiplying both sides of the above equation by $d'$, we get
$$\binom{x}{d} \equiv \binom{y}{d} \pmod m.$$
Note that for $x = 0$ and $x = 1$, we have $\binom{x}{d} = 0$, for any $d \ge 2$. This means in particular that not all $m$ values (remainders) in the period (in the list from $\binom{0}{d} \mod m$ to $\binom{m-1}{d} \mod m$) are distinct, so some remainder must be missing. In fact, we have $\binom{x}{d} = 0$ for $0 \le x \le d-1$, so as this remainder $0$ is repeated $d$ times, it means that at least $d-1$ remainders are missing.
This means that for any $d$, if we take any $m$ for which $\gcd(m, d!) = 1$, there are at least $d-1$ values of $r$ for which the equation $\binom{x}{d} \equiv r$ has no solution.