There are two reasons for this phenomenon. First, it’s much faster to drop a whole big glob on there (and then cut only two thirds of the way through) and second many deli workers feel that their bosses are greedy bastards and that if someone is paying $2.50 for a bagel with cream cheese then by god they should get $2.50 worth of cream cheese.
The only solution I’ve found so far is to buy a bagel with and one plain. After redistributing the cream cheese I typically still have leftover.