Indeed, some authorities, including Tosafot (Berachot 20b) and Rema (187:3), maintain that women do not recite this line of birkat ha-mazon. Tosafot there even suggest that women's inability to say it raises the possibility that birkat ha-mazon is not obligatory on a Torah level for women! Rav Yosef Karo, however, does not express any hesitation about women saying it in Shulchan Aruch (OC 187:4), and Mishna Berura there says it is common custom for women to recite it.
How can reciting it make sense? Three main possibilities:
1. Mishna Berura writes that a woman has in mind gratitude for the gift of berit mila, taking “our flesh” in a broad sense. Though it is performed on men, it is relevant and meaningful to all of us.
2. Beit Yosef writes that a woman expresses gratitude for berit mila because a man and wife are as one flesh. (He doesn’t explain what this should mean for an unmarried woman.)
3. Magen Avraham cites a Talmudic suggestion (A”Z 27a) that women “are considered as though circumcised,” and for that reason can say it. On this last reading, the absence of a foreskin may be seen as an inherent circumcision for Jewish women, who enter the covenant from birth and are grateful for it.