The train firm announced last month that the cost of all journeys would rise by 6%.
Those who travelled yesterday reacted angrily to the new fares, which have also been criticised by consumer groups.
And with more commuters returning to work this morning the increases met with even more unhappiness from customers.
The price of a seven-day season ticket between Kilmarnock and Glasgow has increased from £34 to £36, an anytime day return between Ayr and Glasgow from £12.70 to £13.50, and a seven-day season ticket between Paisley Gilmour Street and Glasgow from £17.50 to £18.60.
ScotRail said it was entitled to increase fares by the Retail Prices Index (RPI) measure of inflation plus 1% and that this was the case for the rise.
The RPI reached 5.2% in November.
Aimee McLean, 22, a bar manager from Anniesland, who travels into Central Station daily, said her return fare has risen by 10p to £2.30.
She added: "It just seems to be going up so often. You get used to paying one fare then they put the prices up again. It's not like we're getting a better service."
Anthony Smith of Passenger Focus, the independent rail watchdog, said the increase did not reflect pay . He added: "The spotlight will really be on operating companies and Network Rail to deliver on their promises about performance and overcrowding.
"Passengers are paying our fair share and we want and deserve better."
But ScotRail defended the move. A spokesman today said the firm "continues to invest in enhancements to meet the increasing demand for rail travel".
He added: "This has clearly been demonstrated, from introducing significant service improvements to adding more seats, including 1100 seats on commuter trains between Dalmuir/Milngavie, Glasgow and Lanarkshire since May 2011."
The increase in Scotland coincides with the Association of Train Operating Companies (ATOC), a partnership of all 24 rail companies in the UK, which announced fares across the UK would rise by an average of 5.9% from yesterday.
A west coast mainline Virgin ticket from Glasgow to London will rise by 8.1%, while the increase on the Virgin Glasgow to Carlisle route is 6.5% – from £46.50 to £49.50.
A Scottish Government spokeswoman admitted "things are getting more expensive, not least because of the price of fuel".
She added: "This government continues to support rail in Scotland with almost 75% of the cost of a ticket paid through subsidies.
"Ultimately, the increase in unregulated fares is a decision for ScotRail to explain to passengers."
rachel.loxton@ heraldandtimes.co.uk
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Chris Raynor, 45, freelance IT consultant, Kirkintilloch: Travels first class every week from Glasgow to London. "I would normally spend about £180 return. But from now on I'll be spending about £200 on a return ticket."
Kelly Hill, 29, midwifery student, Kilwinning: Travels to Paisley every week day. She said: "I used to spend about £33 per week so it will go up by a few pounds. I think they should look at doing a concession for students."
Aimee McLean, 22, bar manager. Anniesland: Travels into Central Station every day.
Her fare has risen by 10p to £2.30 return. She said: "It just seems to be going up so often. It's not like we're getting a better service for this."
Stephen Dickson, 46, bricklayer, Balornock: Now lives in London and travels to Glasgow often.
He said: "It usually costs me about £100 advance so that will go up. But the service is quite good and gets me to where I want to be on time."
