According to Wikipedia, it was targeted by more V-1/V-2 rockets than any other location due to its logistical importance to the Allies. Why was it allowed to be captured intact?
Antwerp was taken rapidly by the 11th Armoured Division when the Wehrmacht was reeling from its defeat in Normandy. In effect, between early August 1944 when the collapse of the German Army in Normandy began, and the re-establishment and rebuilding of the Western Front was undertaken in mid-September, the Germans had very little to stop the Allies, command was in chaos. In short, the Germans were having done to them what they'd done to France in 1940, where plans were obsolete as soon as they were written.
The Germans were fortunate that Montgomery forgot to capture the seaward approaches to Antwerp and it took months to be put into use. The V2 rain was a belated attempt to make good the disaster, but realistically the Germans simply had nothing available to defend Antwerp or carry out its methodical demolition.
It is also worth noting that at this time the German army in Belorussia and Poland had been wiped out and the Red Army was steamrolling almost unopposed toward Germany from the East. The German High Command had a lot going on. And then there's the disruption of the attempt to assassinate Hitler on July 20 1944, which destroyed the capacity of German commanders to show initiative.