In the Chronicle, there was an article detailing some of the financial difficulties that many Catholic Universities are currently facing across the US.
Most of the colleges and universities were founded by orders like the Jesuits or the Sisters of Notre Dame, etc. They relied upon these orders or the church for funding and oftentimes for the physical land and buildings as well! The faculty have traditionally been filled by priests, nuns, and monks who taught for free! Boards also drew upon such pools rather than people skilled in raising money (as at other institutions).
But such unpaid faculty members are in shrinking supply. In fact, there have been increasingly fewer Catholics going into these religious orders since the 60s (correlating with Vatican II). Faculty positions, therefore, are being filled by lay people, who require payment and benefits comparable to their counterparts in other universities. And the boards are not very adept at raising money, meaning that their endowments are small compared to schools of the same size or quality.
The exception to much of this is the University of Notre Dame with an endowment of $5.9 Billion (which is the 14th largest of any college in the country and the largest for any Catholic institution of higher learning).
Most Catholic colleges emphasize affordability (in line with the larger mission of the church to the poor), and so cost less than comparable private universities, but, ironically, due to their smaller endowments, depend upon tuition far more! Hurting the most are the all women's colleges (or traditionally all women's colleges), which, on the whole, receive far less alumni donations than traditionally all men's colleges, and, being founded later than most men's colleges, also have had less time for their endowment to grow.
Nonetheless, many of these institutions are learning the fund-raising game, and are turning things around, at least, according to the article.