Pressure equilibrium means that the pressure of the hot component and the pressure of the cold component are equal at their interface, so that neither expands nor contracts relative to the other. The perfect gas law is $P = n k T$, so pressure $P$ is proportional to both density $n$ and temperature $T$. A cold cloud has low $T$, but if it has high density, it can have the same pressure as a hot, low-density cloud.
Implicit in this is that it is a more or less stable equilibrium, and it is relatively easy to see how this might be. Consider a cold (high-density) cloud embedded in a hot (low-density) medium. If a fluctuation causes the cloud to shrink, its density will increase, raising its pressure and causing it to expand. Or: if the temperature of the hot phase increases, so will its pressure, compressing the cold cloud -- until the latter's increased density (and possibly increased temperature) raises its pressure to point that it balances the hot medium's pressure again.
As for hydrodynamical instabilities: these are not universal, always-on phenomena. For a cold, dense cloud inside a hot medium, the interface will have an inward-pointing gravity vector (pointing toward the center of the dense, cold cloud). This means you have a low-density medium sitting "on top of" a high-density medium, which is the opposite of what's required for the Rayleigh-Taylor instability. (This is why the interface between the Earth's atmosphere and the ocean doesn't suffer Rayleigh-Taylor instabilities.) So: no Rayleigh-Taylor instability. (A cold cloud "sinking" in an external gravitational field is not an example of a Rayleigh-Taylor instability; it's a buoyancy effect, like raindrops falling down through an atmosphere.)
You also probably shouldn't assume that Kelvin-Helmholtz instabilities will instantly or efficiently "shred the cloud". Large cold clouds or streams may be orders of magnitude denser than the hot medium and can have significant self-gravity as well, which will tend to resist "shredding". (After all, the interaction of the solar wind and planetary atmospheres in the Solar System can generate Kelvin-Helmholtz instabilities, but Venus and the Earth -- not to mention Jupiter, etc. -- still have significant atmospheres.)