In Rav Sadiaa Gaon's prayer book, he lists a short prayer for before and and after baths. Why isn't that said anymore (I'd assume it was said in his time)? The text I'm referring to can be found here: http://www.hebrewbooks.org/pdfpager.aspx?req=20685&st=&pgnum=148&hilite=
Saadia Gaon didn't innovate it. It is based on Berachot 60a:
ת"ר הנכנס לבית המרחץ אומר יהי רצון מלפניך יי' אלהי שתצילני מזה ומכיוצא בו ואל יארע בי דבר קלקלה ועון ואם יארע בי דבר קלקלה ועון תהא מיתתי כפרה לכל עונותי אמר אביי לא לימא אינש הכי דלא לפתח פומיה לשטן
Our Rabbis taught: On entering a bath-house one should say: 'May it be Thy will O Lord, my God, to deliver me from this and from the like of this, and let no humiliation or iniquity befall me; and if I do fall into any perversity or iniquity, may my death be an atonement for all my iniquities'. Abaye said: A man should not speak thus, so as not to open his mouth for the Satan.19
Except Saadia Gaon's formulation is more explicit about the danger: "Blessed are You, O God, Who has saved me from the fire."
Given this, there are two obvious answers:
1) Are you in danger from fire when you take a bath? Their bath houses are not the same as our bathrooms, such that the formulation of the blessing, and indeed, the very reason for the blessing (the danger), is uprooted.
2) Even in the gemara, Abaye argues. While Saadia Gaon evidently held one way, perhaps other Rabbinic figures held otherwise.