But in what way does religion directly meddle in someone's life?
Well, let us be clear - religion itself is an abstract concept, not a sentient being. Religion cannot take actions. A religious organization will, in the name of the religion. That's probably what he was speaking about.
I already said that I agree that religion wants to use government to meddle, as do many organizations, (e.g. Occupy Wall Street, environmentalists, etc.). I would agree, also, if someone said religion meddles with government
And since government governs our lives, religion is thus meddling with us. If religious influence leads to a law against who I may sleep with, religion is meddling in my life.
but how does religion skip the middle man and meddle in one's life? (Assuming one is not of that religion, and thereby tacitly agrees to abide by that religion.)
I don't think removing the middle man is required to consider it meddling in my life, but...
How about a church that advises a family to send their kid to Conversion Therapy to cure them of being gay?
How about a religious organization that encourages its members to try to convert young boys, under the auspices of a youth group not run by the organization?
How about a religious organization that digs out personal information on doctors or nurses who work in abortion clinics, and publishes them online?
(The middle one happened to me, personally, when I was a Boy Scout. I was not amused, and had far more willpower than expected, such that it blew up in their faces a bit.).