I donated to Wikipedia before. However, this year, I'm not donating, and my rationalization is this: there need to be more Wikipedia clones on the internet, to best prevent the possibility that a single organization (Wikimedia) abuses its control of the biggest worldwide information source. Thus, instead of donating to Wikipedia, I would like to subsidize potential Wikipedia clones. Whether or not it has ads is of little concern to me.
The main thing I have to say is this: however much you would otherwise have given to Wikipedia, give that money to some other charity. Never make decisions about how much giving to do based on the worthwhileness of individual causes.