However, he said ScotRail's passenger numbers at weekends had bounced back to 2019 levels.
More than £500 million of extra funding has been provided to keep ScotRail trains running during the pandemic, when passenger numbers dipped at one stage to just 5 per cent of normal.
ScotRail has already announced cost-saving measures such as not restoring services to pre-pandemic levels until passenger demand recovered further.
Ticket office opening hours are also due to be reduced at more than 100 stations.
Mr Hynes, managing director of Scotland's Railway, which includes ScotRail and Network Rail Scotland, said: "We have to reduce the net cost of the railway."
He told the Rail North of the Border conference in Glasgow: "At the moment, the amount of money that Government is shovelling into the network is unsustainable.
"On Wednesday, ScotRail's revenue was 45 per cent lower than it was two years ago.
"No business can tolerate a 45 per cent reduction in income and not think about the way it runs its business.
"So whether that's the timetable we operate, the way we sell tickets or the way we maintain track, we need to modernise our railway to reduce the cost.”
Mr Hynes told The Scotsman later: “We do not expect the commuter business to recover for a long, long time because so many people have switched to hybrid working.”
He said ScotRail’s budget under Scottish Government ownership from next month had still to be fixed amid a “huge degree of uncertainty” over future revenue following the “eye-watering” extra subsidy over the past two years.
However, Mr Hynes said ending the requirement to wear face coverings on public transport from March 21 would be a “milestone” towards passenger recovery, which would trigger a major marketing push.
He told the conference that increasing revenue through boosting ticket sales would be also vital.
Mr Hynes said: "I was absolutely thrilled to see that last weekend, our revenue was back to pre-pandemic levels.
"That's an extraordinary achievement, and what it shows is that leisure is bouncing back far quicker than other bits of the market.
"But we have got to think what that means for our railway – a leisure-led railway.
"Maybe it's not a great idea to close the railway for engineering work at weekends. Let's move it to midweek if passenger markets are bouncing back in that pattern.”
Mr Hynes said later that costs would not be cut if it harmed revenue – so extra capacity would be added, such as more carriages on trains “if the demand is there”.
This includes extending more of ScotRail’s Inter7City trains on its Edinburgh/Glasgow to Aberdeen/Inverness routes from four to five carriages, which had been put on hold because of Covid.
East coast cross-Border operator LNER reported a similar recovery trend.
Communications director Kate McFerran told the conference: "It is very much about leisure."
She said passenger numbers had returned to about 90 per cent of before Covid, with Anglo-Scottish journeys "absolutely the busiest".