Since you are married to a Protestant, who has a legitimate share in the decision-making process of the distribution of your family’s church support and charitable contributions, the answer is somewhat different than it would be for a Catholic who is not married to a Protestant.
Although a Catholic should not give to the support of Protestant churches, your Protestant wife certainly may and may feel bound in conscience to do so. Likewise, she may feel uncomfortable giving to the support of the Catholic Church but you are bound in conscience to do so (CCC 2043). As one means of overcoming this impasse, I recommend that you agree on a certain amount of your income for the support of your respective churches and divide it in half. Each of you is then responsible for writing and delivering the check for the amount of money allotted to your own church. (This is one possible way to resolve the situation, but you are free to choose any fair means to which you both agree.)
As a general principle, Catholics should give to Catholic charitable organizations. If there does not exist a Catholic charity doing equitable work to a Protestant or secular organization, the Catholic is free to give to worthy Protestant or secular causes. Again, since you are married to a Protestant, she may feel conscience-bound to give to Protestant organizations. A similar plan to the church-support plan can be created to deal with allotting money to Catholic and Protestant charities.
Should I financially support the projects of Evangelical relatives?
The Catholic Answers Guide to Family Finances by Philip Lenahan