Questions have been asked about £15 million donations to the Green Pastures charity from company dividends when the Co Antrim bus manufacturer was profitable.
Around 1,200 posts were lost after the firm entered administration last week.
Founder Sir William Wright received applause from the workers as he arrived at the church.
Community police mingled with the demonstrators but the atmosphere was peaceful.
Wrightbus had a reputation for building ultra low emissions buses including London’s Routemaster double decker when Boris Johnson was mayor.
It went into administration last week following cash flow problems and the failure to find a new owner.
Jeff Wright, from bus manufacturer Wrightbus, addressed the congregation at the Green Pastures church near Ballymena on Sunday morning.
He said he had not spoken out before for fear of jeopardising delicate negotiations aimed at saving the firm.
He added: “It is a difficult day, it is a sad day”, as he thanked the congregation for all the text messages of support.
Pastor James McConnell, a Belfast preacher, attended the service in solidarity.
Mr Wright displayed a photo of the Wright family 60 years ago with a blue bus.
“This picture represents the heart and soul of what it takes to make a good company a great company.”
Mr Wright said he had fought since he was a 19-year-old apprentice learning under great tradesmen to build the company up.
“We went from crisis to crisis, from when we made money and lost money, but we always tried to keep our quality and integrity as we went.”
He said investing in the property was a “dream come true” because it had the potential to make them into a world-class company.
Over the following years, “blood, sweat and tears” had made the firm great and he said he did not want to jeopardise that now as negotiations to save it continued.
He said his own son, the fourth generation of Wright, had lost his inheritance along with his sisters and their children along with the hundreds of men he had worked, played football and prayed with.
“This is not my church, this is these people’s church, they own this church.”
After the service, company founder William Wright met some of the men standing outside and said: “I am sorry folks, hopefully everything will work out.”
His son Jeff Wright said people who did not know him had said some horrendous things for years.
“There is a time to speak and a time to be silent.”
He said people were working hard to bring in a new investor and receive help from the government.
“I refuse to jeopardise the delicate nature of these negotiations, that could destroy the last chance of saving the workforce and the staff and all the local suppliers.”
He said an evangelical trust held a third of the shares in the company.
He disclosed that £20 million of reserves had been spent on the company over the last year in an effort to keep it in operation until a buyer could be found.
Mr Wright said a lot of people were afraid and scared about the future.
“They don’t know what way to turn, so we must be mindful of that.
“I won’t jeopardise the future so I can look good.”
“I am so sorry that this church has to go through what they went through, I never thought this would happen.”