First of all, suppose $f(1)=x$, then $f(x)=f(f(1))=1$ so $f(1)=f(f(x))=1$.
The set $[0,1]$ is a compact subset of $\mathbb{R}$ and the function $f$ is continuous, then by the extreme value theorem, $f$ must attain a minimum. We can then say that there exists $c\in [0,1]$ such that for all $x\in [0,1]$, $f(c)\leq f(x)$.
Let $b=f(c)$ be this minimum value. By the intermediate value theorem, for any value $y$ between $f(c)=b$ and $f(1)=1$, there is a point $x$ in the interval $[c,1]$ such that $f(y)=x$ because $f$ is continuous. Let $x$ be a point in the interval $[b,1]$, then there exists a point $y\in [c,1]$ such that $f(y)=x$, so $f(x)=f(f(y))=1$. Then for all $x\in [b,1]$, $f(x)=1$.
We defined $b$ as the minimum of the image of $f$. Then for every $x\in [0,b]$, $f(x)\geq b$. We can then evaluate the integral:
$$\int_0^1\!f(x)\,\mathrm{d}x=\int_0^b\!f(x)\,\mathrm{d}x+\int_b^1\!1\,\mathrm{d}x\geq \int_0^b\!b\,\mathrm{d}x+\int_b^1\!1\,\mathrm{d}x=b^2+(1-b)$$
The point $b$ is a value between $0$ and $1$. The quadratic function $b^2-b+1$ is then at its minimum when $b=\frac{1}{2}$. So whatever $b$ is, the integral $\int_0^1\!f(x)\,\mathrm{d}x\geq \frac{3}{4}$.
Finally, the integral cannot equal $\frac{3}{4}$, because if we suppose that the integral is $\frac{3}{4}$, then we know for sure that $b=\frac{1}{2}$. The function $f(x)=\frac{1}{2}$ when $x\in [0,\frac{1}{2}]$ and $f(x)=1$ when $x\in [\frac{1}{2},1]$ will then be discontinuous at $\frac{1}{2}$.
We can then conclude that a continuous function $f:[0,1]\to [0,1]$ such that $f(f(x))=1$ for every $x\in [0,1]$, then
$$\int_0^1\!f(x)\,\mathrm{d}x>\frac{3}{4}$$