I agree with your philosophical view as well. Additionally, good public transit is one of the best investments a city can make. Look at the neighborhoods that have gentrified and people are predicting will gentrify - they almost all have good CTA rail service.
The blog post linked to above works under a couple false assumptions.
The first is looking at the CTA like a business that brings in all it's money through fares and then adjusts expenditures accordingly. That's wrong. For 2007 the CTA will bring in $541 million in fares, contributions from the city, and advertising etc. It will also get $537 million from public funding (RTA, tranfers from state capital funds, etc.). More than half it's budget is completely unrelated to the revenue it generates.
The second assumption is that the CTA has any say in what if offers to "subsidized" riders. The ADA dictates what service the CTA needs to provide to those with special needs, it is not their choice to make based on budget needs.