He told reporters the government should be absorbing the controversy by making it a statutory subject.
Ministers have said they want to improve the quality of PSHE education.
The teaching of sex and relationship education in schools has long been controversial.
All schools are expected to have a policy on sex and relationship education, and to make it public.
But the subject in which it is taught, personal, social, health and economic education (PSHE), is not a statutory part of the national curriculum.
There has been a chorus of demands from teachers, MPs and charities for ministers to change the subject’s status and make it statutory.
Four key House of Commons committees wrote to Education Secretary Nicky Morgan earlier this year, pressing for sex education to be made statutory in primaries and secondaries.
This was in the light of the perceived growing sexualisation of young people and British culture, and the growing availability of sexual material on the internet and in social media.
Mr Hobby said: “We don’t need you need to make PSHE statutory to make teachers do it, but to protect teachers when they do it, because otherwise they are vulnerable to accusations that they are pursuing a personal agenda.
“We’ve seen really difficult situations where parents who disagree with the philosophies that are being promoted are saying, ‘You’re doing this, you’re brainwashing our children.’
“It’s really helpful for professionals on the ground to be able to say, ‘No, this is a duty, it’s government regulation, and I am doing this as every school in the country is.’
“By not making statutory, the government is making teachers absorb the controversy when it really should be the government that’s strong enough to absorb that.”
Mr Hobby gave the example of dealing with topics such as homosexuality in a lesson, where parents may disagree with what has been said.
“These are controversial topics which our society doesn’t wholly agree on, and teachers have to be quite brave sometimes in doing that, and we should have their back when they do that and don’t leave them to have challenges,” he said.
He added parents were wanting to withdraw children from lessons or could make “aggressive challenges” against teachers.
He cited the example of the police having to intervene at a meeting where a head teacher had been barricaded in a room by parents over the issue.