The Church Brew Works has a lot to like. The church architecture gives it a special ambiance. I used to live in the Czech Republic and CBW reminded me of some of the old buildings there which had been turned into restaurants and pubs.
Their beers are good. Their hefeweizen and (currently) their coconut stout are exceptional.
Everything else? Sort of underwhelms me. The food is pricey but the quality is sub-par. I've been there several times in the last year, and tried everything from the soups to the sandwiches to the pizza.
Yesterday I had the lobster bisque, some of my friend's thai wings, and a slice of the mushroom pesto pizza. The bisque wasn't worth the $7 I paid for it. The wings were good, but not great. I thought the pizza was salty and rather bland tasting overall.
I've had other pizzas that were better in the past (from the CBW), but again. They aren't anything spectacular.
The service really varies. I've gone there during a weekday and had to wait forever. Other times, the waitstaff was spectacular.
So in a nutshell:
Positives: Good beer, nice environment.
Negatives: Food quality and price.