  Motivated by the recent observation of CP violation in the charm sector by
LHCb, we study direct CP asymmetries in the standard model (SM) for the singly
Cabibbo-suppressed two-body hadronic decays of charmed mesons using the
topological-diagram approach. In this approach, the magnitude and the phase of
topological weak annihilation amplitudes which arise mainly from final-state
rescattering can be extracted from the data. Consequently, direct CP asymmetry
$a_{dir}^{\rm (tree)}$ at tree level can be reliably estimated. In general, it
lies in the range $10^{-4}<a_{dir}^{\rm (tree)}<10^{-3}$. Short-distance QCD
penguins and penguin annihilation are calculated using QCD factorization. Their
effects are generally small, especially for $D\to VP$ modes. Since weak penguin
annihilation receives long-distance contributions from the color-allowed tree
amplitude followed by final-state rescattering, it is expected to give the
dominant contribution to the direct CP violation in the decays $D^0\to K^+K^-$
and $D^0\to \pi^+\pi^-$ in which $a_{dir}^{\rm (tree)}$ is absent. The maximal
$\Delta a_{CP}^{\rm dir}$, the direct CP asymmetry difference between the
above-mentioned two modes, allowed in the SM is around -0.25%, more than
$2\sigma$ away from the current world average of $-(0.645\pm 0.180)%$.
