I have tested both vehicles quite a bit and actually find the Police Transporter to be more effective overall but I see a lot of people still choosing the riot over the transporter.
With the riot you are much more sluggish allowing for others to easily escape or evade you, furtheremore if someone knows to aim for your tires they can easily limit your movement.
Ontop of that seems the windows eventually break with constant fire turning into big holes that leave you wide open from that side.
Its only real advantage is its resistance to explosions but due to the transporters increased acceleration you can easily move out of the way and dodge most bombs.
Some people claim the transporter is not 100% bullet proof which is true but its still very difficult for players to manage to shoot you given that the gaps in the bars seem to be smaller then they really are if you can even shoot through them, half of the time you don't shoot through. Also these bars do not wear out or break like the riot's windows.