In Toronto this happens all the time and some of the pilots get quite ****ed off about it. 9 times out of 10 I can assure you there is a legit reason. And quite often it is to help you (and us)
First point about the ATIS...if you are landing at an airport with multiple runways then it has the landing runway.s on the atis. Can't just broadcast one if you are landing on two. Then at least as Sid says you can program in both for the 50/50 chance. The ATIS though dosen't have the flow rate and the traffic picture at the point you are entering terminal airspace so all it is supposed to do is give you the options of where you are going to land. The ATIS is giving you the rough idea but it isn't a real time definite. It also dosen't tell you what is going on in the bit of airspace you are about to land in. Problem with a multiple runway airport really I suppose because it means there are multiple reasons why a runway will be changed on you.
At YYZ the runway designation normally depends on the direction you come into Toronto...if we are on the 23/24s traffic from the West and South receives 24R and traffic from the North and North East receives 23. The Enroute sectors into the terminal area will inform the aircraft of this designation well over a hundred miles out. However if there are too many aircraft coming into the terminal area all at once then you have to balance the runway loading. So although you may have been told 24R and have it dialled in...all of a sudden you have become that one aircraft too many and have to be changed to 23. On YYZ terminal we try and do this by 30 miles from touch down to at least give the pilot a fighting chance to program in whatever and check their minima. If (as often happens in YYZ) you end up with too many aircraft on the one runway then you end up flying a lot of extra miles staying up extra high and ending up on a 35 mile final. By doing the "inconvenience" of a late runway change in this instance we actually are getting you on the ground sooner and not clogging up the airspace. We try never to change the runway at 10-15 track miles but if we do it will always be for a good reason..ie birdstrike at airport, slow traffic ahead, pilot cocked up in front of you (and yes that happens....let us know if you want to slow down ahead of time!) too many heavies intermingled with lights and mediums, weather on final..and again the most common in Toronto...too many aircraft in the one small bit of sky. All controllers here will give you the reason and the localiser frequency straight away. We all appreciate the inconvenience to the pilot but the options are nil..unfortunately.
Another case of runway changes is that some aircraft request a certain runway (which you are all entitled to do) to speed up the ground taxi. We again try to be as balanced as possible but if an aircraft requests a non conforming runway for operational safety reasons..ie length then we may have to change runways at the last minute on other aircraft to make space for the non conformer. At YYZ we only do this if it dosen't have a huge knock on effect and normally we can swap other carriers to a runway that is better for their taxi. Some pilots expect this...the ones that don't query..but are always told..it will help your taxi.
Emergency traffic always gets their choice of runway so again if they pick a REAL non conformer then we have to make sure they are safe from the other aircraft coming in to land. That often means aircraft having to slide across from one runway to another..or being switched on first contact. I would expect a fair amount of understanding in this case.
Wind changes. This one is common and you don't normally get any complaint by the aircrew for this.
It is always a balancing act to be as expeditious as possible, and be as fair to the aircrew as possible. If you want to know why your runway has been changed last minute then ask the controller (if he/she hasn't already said)...It will normally be for a quite legitimate reason.
It is another case for fam visits for pilots to visit ATC at airports with multiple runways (not many in UK unfortunately). At peak times in YYZ we change runways on a regular basis...but the pilot could see why we are doing it.
Hope this gives you some idea. At YYZ anyway. The reasons above are interchangeable I am sure with other airports.