Suppose $(X, \mathfrak{A}, \mu)$ is a measure space. Let $\phi$ be a simple function with canonical representation $\sum^{k}_{n=1} a_{n} \chi_{E_{n}}$. I know we define the Lebesgue integral of $\phi$ as $$\int{\phi} \> d\mu = \sum^{k}_{n=1} a_{n} \mu(E_{n}).$$ With domain considered to be the closed interval $[0,1]$, $\int{\chi_{\mathbb{Q}}} d\mu= 0$. But what about if we consider the domain to be $\mathbb{R}$? That is, consider $\chi_{\mathbb{Q}}: \mathbb{R} \rightarrow \mathbb{R}$. I bet its Lebesgue integral is still $0$. The thing I am getting hung up on is that $\chi_{\mathbb{Q}}$ can be express as $\chi_{\mathbb{Q}} + 0 \ \chi_{\mathbb{R} \backslash \mathbb{Q}}$. Then $\int{\chi_{\mathbb{Q}} d\mu = \mu(\mathbb{Q}}) + 0 \mu(\mathbb{R}) \backslash \mathbb{Q})$ and for the latter addend we get $0 \times \infty$, which bothers me a great deal.
My misunderstanding gets a bit more general. What if we consider the space $(\mathbb{R}, \mathcal{L}, m)$, where $\mathcal{L}$ is the Lebesgue $\sigma$-algebra and $m$ is the Lebesgue measure. It's true that $\int{1} \> dm = \infty$ and $\int{0} \> dm = 0$ But, in the latter case, again, we'll have $0 \times \infty$. Finally, if $(X, \mathfrak{A}, \mu)$ is a (not necessarily finite) measure space, $N$ is a set of measure $0$, and $f$ is an arbitrary $\mathfrak{A}$-measurable function, then it is true that $\int_{N}{f} \> d\mu = 0$. For whatever reason, I am having some trouble wrapping my head around this. I think an expert here would be able to read my post and see what's my confusion. Perhaps, I need to see another proof of some of these facts that avoids any situation where $0 \times \infty$ may occur. Thanks!
At least for me, your examples are precisely why we choose to define $0\times\infty$ to be zero. If we didn't, then two different ways of calculating the same quantity would lead to different answers (even if we left $0\times\infty$ undefined).
In the calculation of $\int_{\mathbb{R}}\chi_{\mathbb{Q}} dm$ where $m$ is Lebesgue measure, we can avoid the expression $0\times\infty$. As per the definition you state in the post, if $\phi$ is a simple function, $\phi = \sum_{n=1}^ka_n\chi_{E_n}$, then $\int_{\mathbb{R}}\phi\ dm = \sum_{n=1}^ka_nm(E_n)$. In this situation, $\chi_{\mathbb{Q}}$ is our simple function, so by definition $\int_{\mathbb{R}}\chi_{\mathbb{Q}}dm = m(\mathbb{Q}) = 0$ (i.e. $k = 1$, $a_1 = 1$, $E_1 = \mathbb{Q}$).