Featherstone, who succeeds Dominic Cooke as artistic director of the Royal Court in April, launched NTS in 2006 and has overseen hits including the mutli-award winning Black Watch.
But speaking to the Herald newspaper recently, she said that her Englishness became "a thing" and led to accusations she had deliberately ignored historic Scottish plays.
"It really upset me, because, as with all kinds of bullying, you don't have a voice - so the hardest thing for me was that if people had criticised the programme, I could have defended it, but when people are criticising the programme because I am English, that is indefensible", she said. "What it did, for a short period of time, was paralyse me from being able to be make artistic decisions and I felt defensive."
Featherstone, who gave the interview as she prepared to leave Glasgow for London, revealed the issue came to a head three years ago. "I had a period - not long, because I am very strong - of a few weeks where I thought, 'I cannot do this job - I don't know how to do it,' that I wasn't the right person for it, and I questioned myself because I didn't know how to make decisions any more."
Her comments come in the wake of reports of increased attacks against English people in Scotland, as the country prepares to hold a referendum on independence in 2014. Prominent writer and artist Alasdair Gray recently accused English people who take jobs in Scotland to further their careers of being "colonists".
But despite these issues Featherstone reflected on her six years with NTS as being "totally life changing" and "incredibly inspiring". She called her successor Laurie Sansom, until recently artistic director of The Royal & Derngate Northampton, a "brilliant theatre maker".