You are right that if $E[ |X| ] = 0$, then $X = 0$ a.s. (actually, it's an "if and only if").
Suppose $E[|X| ] = 0$. We want to show $P(A) = 0$, where $A = \{ \omega \mid X(\omega) \neq 0 \}$. Note that $\{ \omega \mid X(\omega) \neq 0\} = \{ \omega \mid |X(\omega)| \neq 0 \}$.
Now, $P(\{ \omega \mid |X(\omega)| \neq 0 \}) = P( \bigcup \limits_{n = 1}^{\infty} \{ \omega \mid |X(\omega)| \geq \frac{1}{n} \}) \leq \sum \limits_{n = 1}^{\infty} P(\{\omega \mid |X(\omega)| \geq \frac{1}{n}\})$
$ = \sum \limits_{n = 1}^{\infty} \int \limits_{\{\omega \mid |X(\omega)| \geq \frac{1}{n}\}} \,dP \leq \sum \limits_{n = 1}^{\infty} \int \limits_{\{\omega \mid |X(\omega)| \geq \frac{1}{n}\}} n |X(\omega)|\,dP \leq \sum \limits_{n = 1}^{\infty} n\int \limits_{\Omega} |X(\omega)|\,dP = \sum \limits_{n = 1}^{\infty} nE[|X|] = 0.$