meaning of Talmud Torah equals all mitzvot

The Mishna in Peah (1, 1) which says Talmud Torah is C'neged culam equals all mitzvot) seems to refer to the 3 mitzvos mentioned previously (honoring parents, gmilut chesed, and bringing shalom between people) where the fruit is in this world and the principal in the world to come . Why do so many people take the mishna as referring to all mitzvos?

Your good question has a good answer: In the Yalkut Shimoni (Mishlei 934), the phrase is used differenntly, without the context of the other 3 or 6 (as found in Pesikta Rabbati, 8) but rather explicitly regarding all the 612 other mitzvot: "All of the mitzvot of the Torah aren't worth one phrase (davar) of Torah, and that's what's meant in the Mishna, v'Talmud torah k'neged kulam" In other words, all the achronim and rabbanim who use the phrase in the broad sense are quoting this Yalkut Shimoni, or maybe are even using the Yalkut to explain the mishna in Peah, as it finishes off there: Haynu Di'tnan... (=this is what the mishna means when it says...)