Delays like the one the OP described on the SFO-BOS trip can, and do, of course happen on any airline. I don't know if one datapoint means it's always better taking a connection on US rather than a nonstop flight on UA (where you at least still get US PQMs).
OP -let's put it another way... Had the flight operated on time...was the rest of the UA experience more or less as you expected? Would you do it again if you knew with certainty (which is impossible, but this is hypothetical) that the flight would operate on time?