Up to 30,000 paying spectators had been told to stay at home on Saturday, as Silverstone struggles to cope with quagmire car parks and traffic logjams.
Qualifying faced a long mid-Q2 delay due to torrential rain and aquaplaning, Lewis Hamilton earlier warning some parts of the layout feature apparently "no drainage".
"That would be a good improvement for next year," he said.
But although historically critical of Silverstone – having once slammed the British grand prix as a "country fair masquerading as a world-class event" – F1 chief executive stunned sections of the paddock on Saturday by defending the venue.
"I'm really, really upset for the fans, but in reality if it was you running the race what would you do?" he is quoted by the BBC.
"They probably couldn't predict the rain."
Ecclestone said wellington boots are not only needed at Silverstone at present, having seen television footage around England of "houses flooded, shops flooded, people abandoning cars".