Despite being a punk rock musician (arguably seen as the antithesis to prog), progressive rock is my primary field of musical interest. I got into it through Yes' album 'Drama' and tumbled down the rabbit hole enough to a point where I'm listening to a handful of new prog releases every month.
I do have great respect for the titans of the "first wave" - mainly Yes and Genesis, but also Gentle Giant, Van Der Graaf Generator, Camel, the Italian bands (Goblin, PFM, Le Orme, etc.) and some Krautrock (Can, Neu!, Amon Duul II, Popul Vuh, etc.) - but I became most enamored with the neo-prog scene of the '80s: Marillion, IQ, Pendragon, Pallas, Twelfth Night...I really dig that stuff, and a lot of those bands, especially Marillion and IQ, have only gotten better with time and keep releasing amazing music. I'm also a massive fan of Cardiacs, they of the Zappa-esque punk/prog fusion, who just blow my mind on every one of their albums.
As far as modern stuff, Porcupine Tree ranks in my top 10 bands and I think Steven Wilson is a legitimate genius. Big Big Train, Anathema, Echolyn, Gazpacho, Anekdoten, Riverside, The Pineapple Thief, Haken and Sigur Ros are a good chunk of modern bands I adore, just to name a few off the top of my head. I listen to a lot of stuff on the Kscope and InsideOut labels. I've really never gotten too big into progressive metal (or metal in general), though I like bits of Pain of Salvation, Opeth and Dream Theater.
As far as Christianity goes, it's definitely a minority in prog, but there are a few good bands. As mentioned, Neal Morse is a master composer; sometimes he's a little too cheesy, but I don't mind his solo work, Spock's Beard or Transatlantic at all. Iona, though, makes absolutely beautiful music and I'd put them at the top of my list even if they're not overtly "rock", and Glass Hammer, when they do dwell on Christian themes, are pretty solid.
Also the band 'IQ' is not there, but I think they are Christian, I saw one of their live shows and the singer was kneeling..
Rush is a great band too.. Their lyrics are not necessarily about God, but they have a lot about love, and of course abstract lyrics.
IQ is not at all a Christian band, and have no Christian themes in their music. Rush have a lot of songs about religion and faith (especially on 'Snakes & Arrows'), albeit through an agnostic/atheistic/skeptical perspective.