He honked because he was delayed by 3 seconds, totally understandable (NOT!)

I've been in similar situations. If I have solid eye contact with a driver and am still unsure whether the driver is going to yield, I put my hand up in a "STOP Sign" fashion. That usually gets the message across that I'm going to continue and expect them to stop. It has worked every time. I consistently do this as I roll through an intersections where opposing traffic may be making left turns in front of me, or where side-street traffic may be making right turns into my lane of travel. You have to be extra vigilant and extra communicative in high traffic areas and intersections.