I too started wirh an entry level bike, Felt F90, and yes its ok to upgrade if you like the bike, I started with brakes, first Koolstop salmon pads, later Cane Creek SCR5s, used off ebay, big improvement.
Next was wheelset, Neuvation M28 AERO3s with kevlar bead tires, this made a huge difference, $250.00 plus tires, then after checking around local bike shops I came across a lightly used Tiagra 9 speed groupset including crank, got it plus installation for $215.00, this included a new Ultegra bottom bracket.
I now have an entirely different better functioning bike that I will ride and enjoy for a long time, it is unlike any other because I choose the component mix and that makes it mine.