If users support these organisations, they can donate directly, especially given that most Wikimedia donors have no idea their money is not being spent on Wikipedia itself.
What is dubious about Arab Reporters for Investigative Journalism (ARIJ), the Borealis Philanthropy Racial Equity in Journalism Fund, Howard University School of Law and the Institute for Intellectual Property and Social Justice (IIPSJ), InternetLab, STEM en Route to Change (SeRCH) Foundation, or the Media Foundation of West Africa? I've poked around to each of them and haven't found any scandals. Do you just not like the values of these organizations? I wouldn't think "dubious" is the right word then. Also, if you didn't like their values, it doesn't make sense to donate to wikipedia, an organization that implements the same values.
If users support these organisations, they can donate directly, especially given that most Wikimedia donors have no idea their money is not being spent on Wikipedia itself.