I try to prove it by contradiction. If the claim is incorrect, then there exist some $f_i=p_i/q_i$, where $p_i,q_i\in \mathbb F_q[x]$, such that $$ \mathbb F_q(x)=\mathbb F_q[f_1,\cdots, f_k] $$
So $x$ is a combination of $f_i$'s. And, I don't know how to continue from this. Please help.
By Zariski's lemma, since the field $\mathbb F_q(x)$ is assumed to be finitely generated as $\Bbb F_q$-algebra, it follows that $\mathbb F_q(x)=\mathbb F_q[f_1,\cdots, f_k]$ is a finite extension of $\Bbb F_q$.
Therefore, the rational fractions $f_i$ are algebraic over $\Bbb F_q$, so that they are actually constants. In conclusion, we would have $\mathbb F_q(x)=\mathbb F_q$, which is clearly not possible (for instance they don't have the same dimension as $\Bbb F_q$-vector spaces, see this).