Religion is and has historically been a large divider of people. It may not always be a divider, and I'm not saying all people of any particular belief system are divisive or exclusive, but religious differences certainly tend to be hot button issues for many people.
The point of a meetup or conference is to bring people together on a particular topic. So unless your purpose is a faith-based exercise, I think it would only dilute the original intent of getting people together for a 'web event'.
As a Dawkins-thumping atheist, I don't think I would mind too much. 'Houses of worship' happen to have some be the most beautifully architectured buildings so naturally make for good venues, irrespective of your religious beliefs or lack thereof.
I do however doubt that any house of worship really wants me in it.
No religion forbids entry into another house of worship. As long as no one preaches or condemns anyone else then there is no harm.
If your place of work instilled a prayer room where all faiths were allowed to use it I'm sure you wouldn't quit your job or refuse entry into the building.
A large part of meetups and conferences is the culture that they foster. Non-partisan venues are more appropriate because the venue plays such a large role in that (regardless of intent).
Besides the obvious impact of alienating some portion of your audience (again, it's inevitable regardless of intent), you're losing an opportunity to build on the culture and possibly comprising what you have built already.
Your government (I'm assuming you live in the USA || Canada) supports "Houses of Worship" through tax exemptions. I'd feel like I was finally getting some value out of a church if a conference was held there.
I have done already...in a way. Reasons to be Appy last year was held at LSO St Luke's and it was actually quite a nice setting. Granted it's not your ordinary church but the building itself was great and had a large enough main room for the conference and little rooms to host coffee's and socialising.
I go to vote at a church hall no one stops me and asks me if I've found Jesus. If I go to a conference the only subjects I expect to hear preached are semantics and semicolons.
If the venue does not require you to listen to their preaching/doctrine , why does it matter? Most of us have to deal with people on topics we don't see eye-to-eye on pretty regularly, why is this case different?
I would be curious if the event or the organizer had any connection to the venue. It wouldn't keep me from going, and it might make me notice it more just for the unexpected juxtaposition.
As the organiser in question. I don't have any religious affiliation. I'm just aware of many wonderful buildings around my citys who's primary purpose is that of worship but design see's them very well suited to a conference.
The point of a meetup or conference is to bring people together on a particular topic. So unless your purpose is a faith-based exercise, I think it would only dilute the original intent of getting people together for a 'web event'.