http://www.torah.org/learning/rambam/tefillah/mt.tf.head.htmlTHE SECOND SOURCE: BERAKHOT 21A
The Mishnah (Berakhot 3:4-5) establish the rule that a *ba'al keri* (one who has had a seminal emission) may not say T'fillah - but does think about/meditate on the words of K'riat Sh'ma while the rest of the community is reciting them. The Gemara (Berakhot 20b-21a) indicates that even if *hirhur lav k'dibur dami* - meditating on something is not reckoned as saying it's, there is still a value in the ba'al keri meditating on the words of K'riat Sh'ma. By doing this, he is joining the community in the matter in which they are engaged (and not separating himself from them). The Gemara then asks: If this is the case, why does the ba'al keri not say T'fillah (evidently even silently i.e. without moving his lips) along with the community? The Gemara (ultimately) responds: Kr'iat Sh'ma is d'Orayta, whereas T'fillah is d'Rabanan (see the various readings of the text in Rashi and Tosafot there). Here we cannot save Rambam's approach as we did before - a baÕal keri is (typically) a case of first thing in the morning - and this T'fillah should, according to Rambam's thinking, be considered d'Orayta. How can we defend Rambam's approach here?
As mentioned, the sugya there is not concerned chiefly with which obligations still apply to the ba'al keri, as much as which words, currently being recited by the community, should also be said by the ba'al keri who is with them. (See the bottom of 20b - see also Otzar haG'eonim, Berakhot p. 50, where a related ruling is cited. The case concerns someone who enters a Beit K'nesset after having completed T'fillah and finds that the community is reciting Ashrei - and the ruling is that he should say it along with them; the basis for this ruling is the Gemara at the bottom of 20b). The words of K'riat Sh'ma are, indeed, directly from the Torah - which is certainly not the case regarding the words of T'fillah.
This response could be challenged on internal grounds, as follows: The Gemara notes that, according to the Mishnah (3:4), a ba'al keri does say Birkat haMazon - and the Gemara explains that the reason is that Birkat haMazon, unlike T'fillah, is d'Orayta. However, it seems that the words of Birkat haMazon are not d'Orayta; so how do we distinguish between Birkat haMazon and T'fillah?
The distinction still may hold, once we clarify the nature of the obligation of Birkat haMazon vs. that of T'fillah. Whereas, even according to Rambam, the Torah only obligates us to praise God, request and thank Him - but there are no specific themes which must be stated. In other words, all of the themes mentioned in T'fillah are created by the Rabbis. T'fillah, in theme and content is fully d'Rabanan.