The side from the war-torn nation were well beaten in their opening qualifier in London in front of a packed house including thousands of Ukrainian fans.
England captain Harry Kane poked home from close range in the 37th minute and Bukayo Saka scored a breathtaking long-range curler three minutes later to all but seal the Group C clash before half-time.
Despite the result, Rotan took positives from the contest against the beaten finalists at Euro 2020.
"I want to thank all the Ukrainian supporters for their incredible signals to the team, the incredible wave of support the Ukrainian team felt every minute of the game," said the caretaker manager.
"I'm also grateful for the support of the England fans because it was an atmosphere like no other international game I have ever experienced and this unique Wembley Stadium atmosphere will give an incredible boost to the Ukrainian players who experienced it first hand."
But Rotan said the current situation, in which Ukraine are forced to play their matches at neutral venues following the Russo-Ukranian war, made it tough.
"The logistics of moving from A to B are incredibly hard," he said. "It takes us almost 24 hours to get together and move to our training camp before the games.
Rotan bemoaned the lack of recent match practice -- Ukraine had not played an international since facing Scotland in the Nations League in September.
"We knew the quality and the strength of the England team but the Ukrainian boys deserve better," he said. "It's a good team and it will progress."
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