What is the convention on color of molecular orbitals in publication figures?
The colours represent the signal/phase of the molecular orbital, i.e. positive or negative.
Below is the HOMO (made with ChemCraft) of butadiene (PBE-D3BJ/def2-SVP with ORCA) as an example.



Figure 1: HOMO of butadiene (cutoff 0.03)

ChemCraft shows by default negative phase as blue and positive as red.
VMD seems to follow the same convention.

You can certainly change the colours if you want.
Below is how the controls for surfaces in ChemCraft look like:



Figure 2: surface controls in ChemCraft

Other programs may use different conventions, such as NBOView (yellow and blue).