Kaipara Mayor Dr Jason Smith said councils were accustomed to people protesting.
"I am also aware there is a silent majority who think differently from the protesters," Smith said.
Rogan, Mangawhai Residents and Ratepayers Association chairman, said he felt angry after making the $115,000 payment.
The money was made up of penalties from once-outstanding rates now paid, and court costs.
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It grew out of 10 years of association-led battling, navigating a complicated legal fight over hugely ballooning costs for the Mangawhai ecocare sewage reticulation scheme.
Rogan said he was now looking forward to heading across the Mangawhai Harbour bar in his boat to catch snapper at the Hen and Chicken Islands – after a pending knee replacement. He would also be writing a book about the saga.
Heather Rogan said they had thought of continuing their battle and not making the payment. But in the past few weeks the couple had realised they did not have the energy to fight any longer.
"I'm looking forward to having more time to catch up with our grandchildren," she said of the end of a fight that had consumed their lives.
Bruce Rogan began the battle with about 100 ratepayers against paying KDC rates over the sewage reticulation scheme. The battle went to the Supreme Court, which ruled in favour of the council.
Boonham, a retired lawyer, said yesterday was the end of a chapter for the Rogans but the Mangawhai sewage scheme cost-overrunfight was not over.
"It is regrettable that the situation has come to this point. We hope this issue ends here so the council can focus on the entire district and plans for the future," Louise Miller, KDC chief executive said.
"We would like to thank Mr and Mrs Rogan for bringing this matter to a close and wish them well for the future."
Mangawhai ratepayers were initially told the sewage scheme would cost no more than $10.8 million when it was announced in 2003, then $37 million in 2009 and up to more than $60 million by 2013.
The scheme's resulting financial burden on KDC led to the Government appointing commissioners to run the council, in what became New Zealand's longest-ever commissioners' tenure.
The Mangawhai Residents and Ratepayers Association exposed illegalities around the way KDC rates were collected toward the scheme's ballooning costs. The Government in December 2013 responded by passing legislation to legally validate their collection. The association-led fight reached New Zealand's Supreme Court, which ruled in favour of KDC.