I bike commute in Boston (Live in Somerville, bike into Boston), and while there's definitely a risk, I feel pretty safe doing so - there are a lot of good bike lanes that make it possible. I definitely agree with your recommendations - need to be very aware of the cars around you (assume everyone in a car is an idiot/out to get you), and I wear a neon jacket, along with lights when it's dark. I definitely feel like it's only a matter of time until I get doored, though. . .
As former Somerville to Boston year round bike commuter (I' now in SF), I just wanted to tell you to rock on and stay safe. :-)
I know a good number of bike commuters in Boston and we've all gone down at some point, some in worse ways than others, but I don't think anyone has been doored too badly, which was always my biggest fear. In my case, I was hit from behind while riding with my lights on in a bike line (Somerville Ave) and thinking I was hyperaware of the cars behind me (the car drove off, but I'm pretty sure it was a drunk driver from the erratic driving). In a friend's case, a police car without its sirens on in JP blasted through a red light and hit him head on. Both of these accidents and most of the serious bike incidents I know of occurred at night. I'm actually more afraid of darkness than doors nowadays.