Idling cars use more gas, drivers have to buy more gas, and therefore pay more taxes.
Frustrated drivers make more mistakes and get more tickets and therefor pay more in fines.
Longer, more irritating commutes encourage more commuters into public transit, where they movements can be better controlled, and provide better leverage for transit strikes.
Need I go on?
Well, that depends on what the lights are attempting to do. It is well known in the utopia of Boulder, that lights are intentionally timed to obstruct traffic flow, because you shouldn't be driving, you should be taking the bus or bike or walking, you eevil gas guzzler. In that case, the lights are timed almost perfectly because they are, indeed, irritating drivers. As an added bonus, they have set up red-light cameras at the most-irritating intersections.
"I often wonder these days with so much technology, why stop lights cannot be better set-up to deal with the flow."
Because you can't violate the laws of physics. Traffic light timing is always a compromise. You have a fixed set of geometrics to deal with, mainly distance between lights and the speed of the vehicles. If you could just focus on one car, you could run him anywhere without hitting a red light - to the detriment of all the other traffic. Smarter computers can only tweak things a little.