So, why is there pro-Morsi protesters? Are they getting paid or gov't employees or what?
The MB has spent 70 years establishing loyalty during oppression by filling in social service gaps left by a corrupt and inefficient government. They've done this while speaking the language of a fervently religious demographic (remember, Saudis may have supplied the money, but it was imprisoned Egyptian intellectuals like Qutb and Zawahiri who provided much of the theoretical framework for 20th century fundamentalism) and while gaining renown for taking up arms against the newly birfed Israeli state even when their government would not.
Consequently, they have fiercely loyal supporters who have waited decades for their opportunity to emerge from the shadows and govern. That's what makes these clashes so much more unsettling. These aren't young military types holding their ground for a paycheck. These are men, women, and children of all ages willing to kill and die for their beliefs and scared that they may be pushed back into the margins. It was surreal to see two groups of people who once fought the police together now being separated by them.
Some Morsi supporters want Shariah, others are just outraged at the perceived insults to their leader. And the MB officials are fanning these flames with a rhetoric chillingly reminiscent of the Castro/Chavez regimes, vilifying opposition protesters as "paid thugs" and "counter-revolutionaries" (the worrisome part for me, personally, is that both sides have conspiracy theories involving US support for the other; the liberals/secularists/Copts believe Morsi struck a "secret deal" with Obama and the SCAF to allow them power in exchange for supporting Israel and not pursuing criminal prosecutions for events during the revolution and the MB believe the US is paying thugs to destabilize the Morsi administration).
