There are some issues that have to be allowed for with FS versus the real world.
Real world - Landing lights (by law) are only required to be installed and a minimum of them working for flight for hire. Company policy dictates when they are on or off and use of other lights, although failure to follow company policy can certainly result in your dismissal (firing). In the real world, the landing lights being on (and the strobes too) during times of low visibility at night are a major hinderance to being able to see out the front and preserving night vision, so there are times that it's better to turn them off.
FlyNET - Landing lights just have to be on in the air below 1000 feet AGL (i.e. they don't have to be on while taxiing) and off above 10,000 feet MSL. As the light flare doesn't affect visibility in FS9 or FSX (which I still don't like that they took that out as it was cool to have), it's not a major deal.
As for the speed, since in the real world breaking the 250 knot limit without permission can cause some serious reprecussions, we put it in. It's a minor ding if you get hit, and it only takes a couple of flights to clear it out.
Don't worry too much about them. They only get to be a problem for you as a pilot if you start getting a lot of them for a while and you drag your overall rating down to a point where you are "undesirable" as a pilot and affect your passenger loads as people get afraid of flying with you.
