Are these increased numbers taking into account the recent protests or will additional spikes occur from the protests?
Not really IMO. I strongly suspect that if there have been coronavirus cases which were spread at one or more protests, it would have hit the news by now. This suggests to me one (or more) of a couple scenarios. IMO the most likely one is that the current spikes, as well as spread into areas which had not really been hard hit yet has little or nothing to do with the recent protests against racism in the US, as they started after the May 25th of George Floyd. That Monday, the 25th, was also the US holiday called Memorial Day which is not unlike Remembrance Day celebrated in other nations to honour fallen service members. That long weekend coincided both with the start of warmer weather across large portions of the US and more widespread relaxation of mitigation efforts , both of which I suspect led to people observing more traditional celebrations for the holiday like gathering with friends, family, and neighbours to have cookouts, picnics, and parties. It is also quite possible that some of these localized spikes had been quietly brewing following protests last month against lock downs and required mitigation efforts. Given that some of those protests took place with people not wearing PPE (or at least not the kind appropriate for medicine) while in close proximity in enclosed spaces/indoors, all of which are factors where the virus tends to spread.
Another possibility is that the contact tracers have been getting stonewalled or lied to about people with new cases having participated in protests or riots and not reporting it. I consider this unlikely due to the simple fact that so many people across the entire country have participated, and no reported cases have made the news as having been likely transmitted at a protest or riot.
A third possibility is that such spreading has happened, but local/state health departments have managed to keep that quiet, and/or news media has failed or refused to report it. I consider this too, to be unlikely. For a set of circumstances like this, I would expect a health department's ability to prevent the information from leaking out to be about as effective as hauling water in a bucket made of metal mesh. Not to mention that there would also have to be a political angle or reason for all the health departments which would be involved to suppress such information. Given that in a number of areas, the local authorities are opposed to the political objectives of their area protesters, it would be unlikely IMO that local authorities would not use such information against protesters and/or carrying out further protests, if the authorities had the opportunity. As for such information either not getting reported, or perhaps suppressed in the media... I doubt that there would be an agreement across the media which would keep them from reporting such newsworthy information. There are just too many stakeholders, with too many different and often divergent objectives for me to believe that something is not getting reported because it does not fit a particular desired narrative. Especially if one remembers that different news organizations have sometimes very different desired narratives.
We are just now starting to get into the right time window where cases which might have been transmitted in the first week of unrest following Mr. Floyd's death would be more likely to be detected. It is also worth noting that while social distancing was often not followed, and masks were not always worn, or worn correctly (as a side note, that as someone with an EMS background, not wearing masks and other PPE correctly drives me up the wall...) and loud yelling/singing/shouting/chanting were frequently involved and tend to shed the virus more readily in such circumstances, most of the protesting took place outdoors in open air, as opposed to confined spaces like indoors/inside a building. Which means that despite the numbers of and close proximity of protesters, the conditions were not quite 'perfect' for virus transmission. An 'interesting' question to ask would be what impact, if any, would the deployment of less than lethal chemical irritants like pepper spray, pepper balls, or tear gas have upon the virus and viral transmission. Given how these agents can make breathing difficult, I could see such agents increasing the spread of the virus. OTOH I can also see the potential for the virus to react poorly to the presence of such agents, which might decrease viral spread.
