You recognized a crucial fact, i.e. that $x^2+x+1$ is a cyclotomic polynomial.
For any $m\geq 1$ we have
$$ \int_{0}^{1}\frac{-\log(1-x^m)}{x}\,dx = \sum_{n\geq 1}\int_{0}^{1}\frac{x^{mn-1}}{n}\,dx = \frac{1}{m}\sum_{n\geq 1}\frac{1}{n^2} = \frac{\zeta(2)}{m}\tag{1}$$
hence
$$ \int_{0}^{1}\frac{\log\Phi_3(x)}{x}\,dx =\frac{2}{3}\zeta(2)=\color{red}{\frac{\pi^2}{9}}.\tag{2}$$
In general, given
$$ \Phi_n(x) = \prod_{d\mid n}(1-x^d)^{\,\mu\left(\frac{n}{d}\right)} \tag{3}$$
we have
$$\begin{eqnarray*} \int_{0}^{1}\frac{\log\Phi_n(x)}{x}\,dx&=&-\zeta(2)\sum_{d\mid n}\frac{1}{d}\cdot\mu\left(\frac{n}{d}\right)\\&=&-\frac{\zeta(2)}{n}\sum_{d\mid n}d\cdot\mu(d)\\&=&-\frac{\zeta(2)}{n}\prod_{p\mid n}(1-p)\\&=&\frac{\zeta(2)(-1)^{\omega(n)+1}\varphi(n)}{n^2}\prod_{p\mid n}p\\&=&\color{red}{\frac{\zeta(2)(-1)^{\omega(n)+1}\varphi(n)\,\text{rad}(n)}{n^2}}. \tag{4}\end{eqnarray*}$$