Because it may be very expensive to operate and maintain? Think about how many employees, water pumps, etc are required to operate that ride?
I don't have the exact data, but it's not like parks remove rides to be Scrooge McDucks for the fun of it.
Or do they?
Also Arrow went out of business in 2002, so that kind of plays role in the Thunder Rapids issues since replacement parts of an old Arrow log flume are hard to find and expensive, but are there other companies that still make log flume rides?