You gave a basic explanation in your question. So explain what you can: that this country speaks to you because you tried to learn its language, that while the situation in her country is bad, this is also amongst the worst crises going on in the world today, and that you're not trying to dismiss the problems in her country by supporting this charity, and would like her support. This would be enough of an answer for many people I know, but not enough for many others.
If it's not enough, the next step is to ask her if she can explain why it's not enough. Does she feel like there's a flaw in your reasoning? Is there something about your charitable giving that makes her feel threatened? Is there something about the charity that causes her to be hostile to it?
If you talk with her about what her concerns are, it can turn out that there are issues she needs answers for that may only be somewhat related to the charity in question.
I've not personally had any partners complain to me about where I've chosen to spend my charitable giving. But I have had a number of friends who have had issues along these lines. While I'm sure that there are people out there who would take issue with their significant other's giving for reasons purely related to the worthiness of the different charities, it so far hasn't turned out to be the case for those cases I'm aware of this happening, and the couple in question talked about it enough to find the real issue.
Several of the partners felt intimidated by the people of their same gender who were receiving the aid. They needed reassurance that their partner was really interested in them more than those other people.
One had some needy relatives who were hoping for help from the charity she was trying to direct his attention to. She didn't feel comfortable asking for help for her relatives at that early stage of their relationship. This would have been enough to get him to change his charitable giving for a little while, but probably more directly at her relative, so as to be able to return to giving to those he felt needed it more in the abstract sooner. But in this case, that story didn't come out until after they'd broken up.
Several had received mistreatment at the hands of some people of the group they believed were getting the benefits of the charity. As it happened, they'd actually received rough treatment from the same people who were causing the problems for the people being helped by the charity. But either way, it was a case of judging an entire cultural group within a country by the acts of a few expatriates of that country.
Asking these people what their concerns were never itself seemed to reduce the conflict, but they revealed information that made it more possible to resolve the conflict.
Different people are incredibly varied, so I'm sure there's a lot more reasons than just the few I've encountered here. I've heard rumors of many others, but I haven't been close enough to those stories to feel comfortable claiming them as some kind of "this definitely happened".
If she won't talk with you about it, but she has some close friends who will, talk with them and see if they understand why she's as upset as she is about this.