When I tried to enter frequencies in my 2 meter YAESU, it was already programmed for 144.000 MHz as the primary. WHY?
You'll have to be more specific about what “the primary” is (give your radio model and the exact words/labels it uses in your question) for a more definite answer, but most likely it's simply that 144.000 MHz is the lowest frequency that is part of the 2-meter band (this is true worldwide), so it's a reasonable place to start for a VFO which has got to have some frequency to be on.
Note that you should not actually transmit on 144.000 MHz, because it is the lower band edge, and so the lower sideband of your signal would extend outside of the band.
It's just the default setting. You can change it either through the menus or with the software, depending on which model radio you have.