As the chief executive, Thompson, who was unanimously appointed to the director-general's job by the BBC's board of governors last week, attracted much credit for putting Channel 4 back into profit and fending off the threats from multi-channel by re-investing in its core schedule.
Mick Perry, the chairman of Magna UK, said: "I'm disappointed that he's going - he had a commitment to original drama, which is what we want to see more of from Channel 4. And from a business point of view, Thompson has cut out some of its extensions and has put its eye back on the core channel."
Despite Channel 4's share of viewing slipping below 10 per cent for the first time in its 21-year history, Thompson is credited with running a steady ship following his decision to scale back its loss-making 4Ventures division and invest more in programming.
"The share has been unbelievably steady. Channel 4 is still seen as youthful, funky and edgy and a real opportunity for advertisers. I think Thompson did a pretty good job," Jim Marshall, the chairman of the IPA's media futures group, said.
There is also hope that as the BBC starts the review of its Royal Charter, Thompson will concentrate less on beating its commercial rivals in the ratings war and more on fulfilling the terms of its charter.
"The advertising world wants to see a balanced and healthy BBC and, of course, it needs to be involved in the popular end of the market as well as with public service broadcasting. But I'd hope that Thompson avoids the more nakedly ruthless and ratings-obsessed approach of the previous regime," Marshall said.
Perry agreed. "I'd like to think that under Thompson it will be a less ratings-focused BBC, although, compared with Greg Dyke, anyone could show more restraint."