The U’s spent the majority of the campaign inside npower League Two’s top seven, but a dismal run of results in the final weeks of the season proved very costly.
The club have spent this week analysing their ninth-place finish and which areas need to be improved for next season.
Changes are planned on the playing side, but one area of continuity is in the manager’s seat, with Wilder set to begin his fourth full season with United in August.
Thomas said: “Absolutely, I think Chris has shown over his time here that he can continue to improve.
“There are a lot of circumstances in football that you can’t legislate for and some of the injuries especially were part of that and came at bad times.
“There are a few things that have gone against Chris, but as a club we know how hard he works.
“We’ve got to make sure we give him the help he needs and not panic, because we didn’t achieve our goal.
“Chris knows as well as anybody that we didn’t achieve what we wanted, but we weren’t that far off it and we’ve got to make sure we get there next year.”
Wilder received criticism from a section of the club’s fans as results deteriorated during the run-in.
The 44-year-old remains deeply frustrated his side are not in the play-offs, which start today, but is fired up to come back stronger next season.
He said: “I’m possibly more determined than I’ve ever been in my managerial career to take us to where we want to go.
“People will always question the job you’re doing and expect more at every level, whether it’s (Sir Alex) Ferguson, (Arsene) Wenger, everyone.
“There will always be people that want a change, it annoys me at times because I think some people are very dismissive of the jobs people have done.
“Everybody has always talked about the stability at this club and we’ve had another season of improvement.
“But for every one that’s dismissive there are four or five who are supportive.
“I put more pressure on myself than anyone else does to succeed.
“I’m a very driven person and I’m absolutely gutted that we’ve not got in the play-offs because we worked extremely hard to get there.”
Wilder joined the U’s in December 2008, guinding them to promotion back into npower League Two via the Blue Square Premier play-offs 18 months later.
After three and a half years in charge at the Kassam Stadium, the former Halifax Town boss is now the 11th longest serving manager in the top four divisions.