Let $X$ be any locally compact Hausdorff space, and $\mu$ be a positive finite regular (both inner and outer) measure on $X$ such that $\operatorname{supp}(\mu)$ is compact. We have that $$\int_X f \ d\mu = 0$$ for each $f\in C_c(X)$.
Then can we conclude that $\mu =0$?
I was trying to find a counter-example, but am stuck at some technical issue.
Yes, you may.
Note that $I_\mu : C_0(X) \to \mathbb{R}$ given by $I_\mu (f) = \int_X f d\mu$ is a continuous linear functional. Since $C_c(X)$ is dense in $C_0(X)$ and $I_\mu$ is zero on a dense set, it must extend uniquely to the zero functional on space $C_0(X)$. But the zero functional is represented by integration against the zero measure, so $\mu = 0$.