It’s never acceptable to discriminate or be hateful toward a group of people, even if you are a member of a minority or oppressed group. Equality means that EVERYONE deserves to be respected for their identity, and this includes people who are born cis.
Ask your friend to avoid making blanket and sweeping statements. There are transphobic trans people, and there are transphobic cis people. Remind her that you are not attacking her by requesting this, but as a cisgender person you have the right to have your identity respected as much as she does. Try to suggest some re-phraseing techniques: instead of “cis people are transphobic” say “there is transphobia”.
There are ways of speaking about identity politics without making generalizations and targeting groups of people/identities, and it is these methods that are the most productive in establishing a useful dialogue because they don’t hypocritically alienate people and therefore open people to really listen to what’s being said.
I hope this helps, best of luck!