I understand that in general the Protestant estates of Bohemia were anxious that Ferdinand might take away some of their rights granted by the Letter of Majesty, but according to Martinitz's account the crowd that barged into the council chamber were upset that "His Imperial Majesty had sent to their graces...a sharp letter" which "declared all of our live sand honor already forfeit". What exactly was this letter that got the Protestant estates so spooked they felt they had to toss a few lord regents from the window? Also it seems odd that the letter came from "His Imperial Majesty", meaning Matthias instead of Ferdinand--why would the Emperor be giving orders to the regents of Bohemia instead of the King?
Source for the quotes is "The Thirty Years War: A Documentary History" translated by Tryntje Helfferich
The (in)famous "sharp letter" (known in Czech historiography as "těžké psaní") was Matthias' response to a resolution send to him by the Bohemian protestant estates on 6th March 1618 that demanded uphelding Rudolf's Letter of Majesty (which was in their opinion being violated) as well as calling the next session of their own protestant-only assembly on 21st May 1618.
It is worth noting that the resolution did not blame the Emperor himself rather than the regents in Prague, in fact it was first adressed to them. The regents however refused to even admit the delegation carrying the resolution, so the Protestants decided to send it directly to Vienna.
The Emperor's response was swift and relatively harsh, to the point that some of the Protestant estates suspected it was written in Prague rather than by the Emperor himself; basically he in relatively hard language denied all of their demands and forbid calling any further assemblies by the Protestant estates under the threat of a severe punishment.
The Protestant Estates while shocked by the response, were not dettered by it and called the assembly anyway. A day after the assembly (22nd May), the leading figures of the Protestant estates held a meeting in which they decided to storm the Prague Castle the next day and defenestrate the regents. The rest of the story you already know.
Now, to your second question: the resolution was sent to Matthias because technically Matthias was still the king of Bohemia - to clarify, while Ferdinand was indeed elected and crowned as the King of Bohemia in 1617, it was done on the grounds that he would be the successor to Matthias after the latter dies (as Matthias was childless and with regards to his age it was unlikely that he would ever have children) rather than replacing Matthias on the throne outright. Thus Matthias never abdicated and in 1618 was still the King of Bohemia until his death in 1619.
Source: PETRÁŇ, Josef; Staroměstská exekuce, 2004