This is somewhat of an opinion-based question. So, my answer will be primarily opinion-based as well.
Pro Bono means for the good of all. There are many non-profit or not-for-profit organizations which are not "for the good of all" but rather the "good of our select group".
It's important to first realize that many non-profit organizations still make a profit. The difference is their tax status and the idea that they reinvest the profit into the organization rather than distributing dividends to shareholders or owners. That does not mean they have no money. Many "non-profit" organizations pay their employees very handsome salaries. You may be interested in the salary studies for nonprofit executives (view the PDF link at that page).
I'm generalizing here. There are non-profit organizations which are solely focused on their mission. But I feel it's a common misconception that "nonprofit" means "no money".
My point is many nonprofit organizations are merely businesses with a special tax status. That does not mean they can't afford to pay for services just like any other business. They all ask for reduced pricing or free work, but the reality is they have funds they could allocate if they saw the need as important enough. This is no different than any client I've ever come across.
That being posted....
I have donated services.
I have worked at reduced pricing for some organizations.
I have worked at full rate for nonprofit organizations.
I do not see any detrimental aspects to working for nonprofit organizations you believe in and wish to support.
Donating specialized services on a volunteer basis (or reduced cost) is merely one way you can give to charity other than your physical presence. In fact, it is often a better use of those with specialized skills the organization is in need of. Grassroots.org is an organization specifically designed to match up those with special skills with non-profit or volunteer organizations in need of those skills.
It is important to treat any donations or reduced cost work as real work though. With full project specifications, timelines, and budgets.
You need the full project scope so you can cap what you are doing and prevent the ever-running project scope which may happen. Set hard milestones or finalization factors and once they are met close the project. Don't let the organization stray, they will tend to without any direct malice. You need to manage them because without pricing involved, they may tend to just keep asking for more. You can always work on multiple projects, but don't let it become one ever-increasing morphing thing.
Really the only difference on your end should be the invoice. Either it is due or not. If you have an agreement to donate services, it's a good idea to still send the invoice but mark it as "donated" or indicate a discount if working at reduced rates. This way the organization has an understanding of what you are doing for them beyond the actual work.
Even if you don't charge the organization a penny, you need to have them agree on the price of what you are providing (tax purposes). If you donate a $500 item to your local Goodwill (assuming US locale) that is a tax deduction. Check with your accountant, but any donated services may also alter your tax situation depending upon the organization.
In short, No. I do not believe supporting any nonprofit or not-for-profit organization you wish to help is detrimental to any industry as a whole. It is only working for commercial, sales/service, profit-driven, businesses which lowers the standards other clients have for freelancing. And to be honest all the "contest" sites on the web do more harm there than you ever will.