In saying that "all are punish'd," Prince Escalus is pointing out that all the citizens of Verona have suffered due to the long-standing feud between the Capulets and Montagues, and also due to the Prince not putting a stop to the violence sooner. Not only did Lords Capulet and Montague lose their children, Prince Escalus also lost his family member, Mercutio, due to Tybalt. Hence, not only were Capulet and Montague punished through the loss of their children, Prince Escalus was punished as well through the loss of Mercutio for not ending the fighting sooner.
The citizens of Verona were also punished. Not only did the feud disrupt their peace and create whole-city riots, as we learn in the very first scene, but the Capulets and Montagues were actually highly esteemed public figures. We learn that Verona thinks highly of both families when Paris refers to their honorable status in his line, "Of honourable reckoning are you both" (I.ii.4). Not only that, Capulet comments that all of "Verona brags of [Romeo] / To be a virtuous and well-govern'd youth," showing us again that the families are thought very highly of (I.v.70-71). Therefore, not only will the Capulet and Montague family members grieve over the loss of Romeo and Juliet, but all of Verona will grieve with them. Hence, we can say that the whole city has been punished for fueling the feud with their own fighting, rather than trying to put a stop to it.
Finally, even though Prince Escalus tells Friar Laurence that, "We still have known thee for a holy man," meaning that the Prince Escalus and the rest of the witnesses still believe the friar is innocent and still worthy of serving the Church, Friar Laurence will still have a great deal of grief and even some guilt to face (V.iii.281). Namely, Friar Laurence will grieve over the loss of Romeo and Juliet, but he will also feel guilty because his plans that went awry are partially responsible for their deaths. The first plan that went awry is that he married them with the hopes that their marriage would end the feud. The second plan that went awry was Juliet's faked death. Hence, although Lords Capulet and Montague are ultimately to blame for their children's deaths, Friar Laurence will not be able to completely rid himself of guilt, making him another punished character.