With tax dollars going to fund federal programs that aid the needy, can any portion be considered tzedakah?
Answer
The Taz says (Yoreh Deah, the beginning of siman 249) that one cannot use his ma'aser money to pay taxes even though the Gemoro B.B. 9A calls taxes tzedaka. See the Maharsho thereon who explains that the reason taxes were called tzedaka is because they took from the wealthy in place of the poor. Therefore, the situation is similar to your situation and yet the Taz rules that one can't use ma'aser for this.
Furthermore, only a tiny portion goes to programs that could be classified Halachically as Tzedaka. Furthermore, see Iggros Moshe (Yoreh Deah 1,149) that one can't give his tzedaka funds to the Federation because they don't handle the money as directed by the Torah.