A couple reasons....often certain ones, esp bulkhead, exit row, and those considered "desirable" are held so accomodation can be made for pax w/special needs(e.g. a raisable-armrest aisle seat for a disabled individual)...maybe bulkheads for pax w/little ones (much easier to manage them if no one in front of you)...exit row for particularly tall folks, etc. Also, when the the possiblity of a late flt w some cnx pax to yr flt, some will be held for the gate-to-gate customers. This can also depend on the booking class of yr tkt....if you are on a bulk (Priceline, Hotwire, etc), preference may be given to AAdv (or Elite, whatever) pax or those w/full fare tkts. Sounds unfair, but overall it's reasonable. If you think of it like this.....you reserve a car w Hertz for $20 a day and .15 per mile....someone else pays $35/.25, its reasonable to assume the higher rental wd be, say a Town Car, where the cheaper one is a Cavalier. 1st come, 1st serve isn't always the case. Hope this clarified at least some of your question.....there are other reasons specific for each situation.
I remember when......a plane trip was a big deal.