When we say a polynomial is irreducible over $\mathbb{F}_{q}[x]$, what we mean is that it does not factor (and therefore has no roots) in $\mathbb{F}_{q}$. It will factor over an extension field, basically there is a larger field containing $\mathbb{F}_{q}$ over which the polynomial will factor. One interesting result is that all fields of order $q^{m}$ are isomorphic, so any irreducible polynomial in $\mathbb{F}_{q}[x]$ will factor completely in an extension field of order $q^{m}$.
One way to think of this, there are irreducible polynomials in $\mathbb{Q}[x]$ such as $x^{2}-3$, $x^{2}+1$, $x^{4}+x^{2}+x+1$, but all of these polynomials will factor completely over $\mathbb{C}$. However, the behavior is a bit different here from the finite field situation, because there are many different nonisomorphic degree 2 extensions of $\mathbb{Q}$. For example, $x^{2}-3$ factors over the degree 2 extension $\mathbb{Q}[\sqrt{3}]$, but $x^{2}+1$ does not.