One important thing to remember is that heat doesn't cause damage until around 140% heat, so you have plenty of range to play around in.
v 1.2 Update: The new heat mechanic in 1.2 has moved the heat goalposts around, meaning you now start taking damage to modules at 100% heat and damage to your hull at 140% (or the second line on the new heat bar).
 - The point at which you hit 100% in 1.2 is the same point you would have hit ~140% in previous versions, so you are not at a higher risk, it's the measurement that makes more sense.
The video guide is still relevant in 1.2 and higher, just bear in mind the above about the heat numbers. i.e. don't go above 100% any more.
How I've always done it
The way I usually fill up my tank is to aim first, have the star just on the edge of your view then throttle down to zero. When in supercruise this does not mean stationary so adjust your angle in small increments so that your heat stops rising but you are still getting a decent rate. If you are in a hurry, adjust your speed up in small increments as well which will give you a better rate but increase your heat, so you have to keep watching.
When scooping a lot of fuel, there's not much you can do about it other than find a good angle then go read reddit whilst you scoop.
Rate vs Scoop size
Each size and class of scoop will have a different rate and finding the optimal for your currently fitted scoop will take some experimentation. As above, until you know what a "safe" rate for your scoop is, just slowly increase the rate by adjusting your speed or angle against the star until your heat stabilises at a value less than 100%.