During the Renaissance and to an even greater extent during the Baroque, Organ was a very popular instrument among classical composers. It was used mostly in sacred music, but most composers at this time were writing sacred music.
In the Classical era, more composers were able to break away from the Church and create and sell their music independently. It seems, though, that Organ remained almost exclusively for liturgical music.
I'm not claiming that no secular music was written for organ, but wondering why it was not more popular. It seems that the huge variety and range of sound available on the great pipe organs of the late 19th century would have attracted composers like Wagner, Strauss, Debussy, and others of that time.
Source: The Harvard Dictionary of Music Don Michael Randel (Organ entry is on page 603, not shown in the ebook unfortunately)
I am thinking of this because of this video of contemporary organist Cameron Carpenter explaining his arrangement of Rachmaninoff's Paganini Rhapsody. The various colors, dynamic range, and pitch range seem like they would have been very attractive to these composers. Why did these composers not make use of this instrument at the time?
You kind of answer your own question in your post. Pipe organs are massive, expensive affairs that were typically only located in a church. They're also completely stationary, and can't be moved out of their location once installed. So, if you're a church, you're going to be able to commission a work that includes an organ. However, if you're a nobleman, without a VAST amount of wealth, you're not going to buy a cathedral organ for your house. Even if you have that kind of money, it wouldn't make sense to have an instrument that large and loud in a private home. Far more sense to buy a harpsichord, or later, a piano. If you're going to host musicians for a concert in your home, it's going to be a group of chamber players, and would not include a pipe organ. As music moves more into private hands and out of the church, private commissions would become more common, and also, less organ music. And if you're a composer writing without a commission, if you write a piece for organ, you're very limited in the places it can be performed, whereas if you write a flute sonata, or art song, it can be performed virtually anywhere, and will likely be performed more often, and you can sell more copies, and more tickets.
Even today, the only place you'll be likely to find a pipe organ outside a church would be in a huge concert hall, and it's usually only performed for symphonic works that include organ, which are also more rare, because you need some pretty big symphonic forces to be heard over the sound of a cathedral organ (Mahler's 8th symphony, for example).
tl;dr, organs are big, heavy, expensive, and loud, and most people don't have them.