His comments come as a survey published today by management consultancy firm Hay Group reveals that "hardest-hit" workers could expect to spend an average of 8% and in some cases up to a third of pre-tax salary on transport costs in 2013.
Hockaday told HR magazine: "Unfortunately the railway is playing catch-up from under-investment during the 1980s and 1990s and must now focus on improving the travelling experience after years of neglect, so these rises were always going to happen and will continue to rise quicker than people's salaries for at least another couple of years."
Hockaday added: "The books currently don't balance but a lot is being done to save costs and not put the whole burden on the commuter.
"Nobody in the rail sector wants to price people away, it's not in their interest to do that."
Hockaday said HR could go some way to mitigating the effects of the fare rises. "Employers could offer initiatives such as season ticket loans; it's something we introduced at LOROL and I know staff appreciated that," he said.
"Another opportunity would be to let workers start the day early to avoid peak fares. It's these sorts of initiatives that can help ease the pressure on workers."
The rail fare rise of 4.2% (on average) that came into effect yesterday will put the average annual season ticket at £2,191 or 8% of the median UK salary of £26,082, said Hay Group.
However, the survey did reveal that towards the end of last year pay increased by 3.5%, outstripping inflation and boosting real pay for the first time since 2009.
Adam Burden, consultant at Hay Group, said: "As the cost of commuting continues to rise faster than wages and inflation, employees are becoming increasingly concerned about the significant proportion of their salaries they lose to travel.
"It isn't all about pay, there are affordable measures that organisations can take to help employees with the mounting 'commuter crunch', including flexible working, the opportunity to work from home or season ticket loans."
Burden added: "In addition, employers who are concerned about losing key talent should ensure they measure employee engagement effectively and also consider offering more development opportunities such as training or promotion."
TUC general secretary and chair of campaign group, Action for Rail, Frances O'Grady said: "I understand the frustration felt by many commuters going back to work today. At a time when real wages are falling and household budgets are being squeezed, rail travellers are being forced to endure yet another year of inflation-busting fare increases.
"As well as having to shell out record amounts of money for their tickets, passengers also face the prospect of travelling on trains with fewer staff and having less access to ticket offices. They are being asked to pay much more for less."
Transport minister Norman Baker said the Government had intervened to reduce the scale of the rises.
He said: "Family budgets are being squeezed, so that is why this coalition Government has taken proactive steps to cut the planned fare rises from 3% to 1% above inflation until 2014."
He went on: "We are engaged in the biggest rail investment programme since the 19th century and it is only right that the passenger, as well as the taxpayer, contributes towards that.
"In the longer term we are determined to reduce the cost of running the railways so that we can end the era of above-inflation fare rises."
