She literally says as much immediately after that sentence:
Python:
my "I never felt this comfortable with Josy."
mc "Oh?"
my "I think it's because of Dad."
mc "Yeah, I get it."
my "Or at least that's what I keep telling myself."
mc "..."
my "*{i}Sigh{/i}* That didn't come off good."
my "I wanted to say that this - you and I - feels great. That's all."
Patrick has definitely managed to impose his views on Maya to some extent, at the very least to the point she would consider him a potential factor in her discomfort. Maya has been forced to hide her relationship with Josy from him and dread the possibility he finds them out for months, it absolutely shouldn't be even a question such thing might affect her sense of comfort when she's together with Josy.