Doncaster was named chief executive of the merged league earlier this week after beating Scottish Football League chief executive David Longmuir to the post.
Some lower-league clubs had issues with the Scottish Premier League and Doncaster in particular during the Rangers saga last summer and the reconstruction process, with some describing the merger as an SPL takeover.
But Doncaster feels the organisation will work for the benefit of all the professional clubs.
"I think this is definitely a new beginning for the game in Scotland," he said.
"For the first time in 15 years we have a single league covering all 42 top clubs.
"We have to demonstrate to all 42 clubs that we are there for all 42.
"We have a board where half of the club representatives are drawn from what was previously the SFL.
"It's absolutely clear that the role of the SPFL is to look after and safeguard the interests of all 42."
Doncaster added: "I believe that Scottish football is in a better place with one league body being able to have a single conversation with broadcasters, sponsors, government, the Scottish FA.
"All of those conversations are important and it's far easier and far better to have one conversation rather than a number."
The merger was only ratified last week - almost six months after a deal was agreed in principle.
The explicit threat of an SPL2 breakaway by First Division clubs appeared to persuade some clubs in the bottom two tiers that they had no option but to vote for the merger, but Doncaster claims he was always confident of a deal.
"I always believed that we would get to the right answer," he said.
"Ultimately if what is being proposed is right for the game and is right for the country and is better than what is there at present, then it's only a matter of time.
"I think at the point where we got unanimity among the 12 top-flight clubs, we really believed we were on the verge of being able to achieve the change that Henry McLeish had recommended (in his report on the state of the Scottish game) and the supporters wanted."