If you sync your secrets to some cloud service then yes, you are trusting that cloud service. And if you let your TOTP cloud service reset your account with an email then it probably isn't the most secure option.
But the important thing here is that the user is in control. They can memorize their secret if they want to an no one can take it from them. Or they can publish it online if they don't like security. With SMS 2FA you need to trust your telecom provider, I very much don't.