Car insurance policies even the comprehensive insurance ones, do not have a "force majeure" clause included in them. As such, I would say insurance companies may be right in not bearing the cost of repairs of your car damaged due to water-logging or natural calamity. Your argument that the damages were due to man-made water-logged areas is not valid and will not hold should you take legal action. If you want protection from such natural calamities in future, have the "force majeure" clause included in your insurance cover for an additional fee, and you can sleep peacefully.
Many years back, Riyadh in Saudi Arabia received an unexpected hailstorm which was the first in known memory. Hundreds of cars got pockmarks all over them when they were struck by hail. None of the insurance companies paid for repairs.