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but most of them aren’t protected

That said, the North end has a wonderful separated bike lane.

Well there I part ways with a lot of local pro-cycling opinion. Separated lanes are only superior under tightly controlled design, and most around here are far from that and give an entirely false sense of security. They're often hidden behind parked cars and every intersection is highly stressful minefield of interactions with drivers completely unaware of your presence. That Commercial St path in the North end is not separated at all from pedestrians and is (belligerently) considered by most joggers to be a their path, and pedestrians don't think of looking before lurching into it unpredictably. Even the stretches where the pedestrian area is 15-20ft wide, the majority of joggers use the bike path, and where it's crossed by side streets and parking entrances, cars will just blow through your path.

The Seaport Blvd "separated lane" is f'ing lethal. The Somerville Beacon St lane made things significantly worse IMO. I commuted that regularly before when there was just a big wide lane rideable without any drama or difficulty. After the new lane I only rode it 30 or so times and with the near misses I experienced or witnessed mean I avoid that route eastbound if at all possible. Now it's a hidden lane behind parked cars where motor traffic often doesn't notice cyclists and blows right across your path.

Separated lanes are the ideal when they're done right, following best practices, e.g. from the Dutch, which means not on roads with many crossing intersections, and at intersections the lane needs to be carefully managed with a significant period pulled out clearly beside the motor traffic lane before the crossing.

After a dooring 18 years ago I've been very careful passing parked cars in general, but a false sense of security in a segregated lane, and a brief failure to recognize the danger, means I was doored again 3 months ago, from the left. Frankly it just confirmed what I've been feeling over the last few years about unsophisticated "separated lanes good" attitudes. A lane painted alongside traffic is often not inferior in reality, in my experience, even if (and sometimes because) it doesn't make people feel so secure.