Due to the on-going strike action in and around Quito, president Lasso declared a state of emergency in that part of Ecuador yesterday. While there is little threat of violence - it has become difficult to move freely in and around the capital due to road blockages.
If you must travel via Quito to Galapagos in the coming days, you should be OK as long as you don't stray too far from the airport if you have any free time / staying on the continent for a few days.
Options including finding a hotel very near the airport if you need one, or re-routing through Guayaquil, which is not affected.
Based on my near 25 years of experience monitoring Ecuador, such protests do occur from time to time, and usually last between several days to a week - 10 days.