I teach courses to nonprofit leaders on using the Internet for outreach, advocacy and fundraising. One part of that course concerns obtaining domain names including from the secondary market. I usually ask the audience to tell me how much they spent on the last three promotional mailings they sent to constituents including the cost of printing and mailing the piece. The number quickly gets above $10,000. I then ask why wouldn't they spend that or even more on a domain name that could be used for years to come without printing or mailing expenses and that constituents could use to read about their work, make donations, or interact with staff? Suddenly they get it.
Nonprofit organizations pay for lawyers, accountants, fundraising and management consultants, office rental, electricity, water, printing, newspaper ads, insurance, airline tickets, etc, etc. I have signed multi-million dollar contracts with nonprofit organizations for consulting and there are even nonprofits that spend more than $1 million annually on PPC advertising. They do not receive discounts for most of these expenditures. It is the cost of doing business.
The New York Stock Exchange gave their chairman a pay package of more than $100 million dollars as a nonprofit organization. (ok, that was more of a fun-fact) and there are seven and six figure salaries paid in the nonprofit sector at universities, hospitals, arts organizations and others.
If instead the organization had contacted you about donating money and not a domain, would you have given a sum equal to the value of the domain?
Anyway, if you believe in the work of the organization and choose to donate the domain then fine, that is noble. If not and you choose a fair profit, that is fine too. You could even use some of your profit to donate money to a cause in which you strongly believe.
Good luck with your decision.