In the early days, very few people interacted directly with database systems, although without realizing it they interacted with databases indirectly — through printed reports such as credit card statements, or through agents such as bank tellers and airline reservation agents.
Let me begin by minimally describing this sentence grammatically. (according to The Perrin-Smith Handbook of Current English)
In the early days, very few people(Subject) interacted(Verb) directly with database systems(Object), although(Subordinating Conjunction) without realizing it they(S) interacted(V) with databases (O) indirectly — through printed reports such as credit card statements(Subordinate Clause), or through agents such as bank tellers and airline reservation agents(S C).
If a set of people (very few in number) interact directly (see below) with a database, by definition*, they are aware of it.
People who interact indirectly with a database, may or may not be aware of it.
In the original passage, 'they' interact with a database 'without realizing it'.
Logic dictates that these two groups of people are separate and distinct from each other.
*directly: plainly and without implication (Webster's Third New International Dictionary)
There is a grammatical problem in the original. In order for a pronoun to be clearly understood, there must be a clearly understood antecedent. In other words, a noun to which the pronoun clearly refers. Again according to Perrin-Smith, 'The antecedent of a pronoun should be a definite noun, not one that is implied'.
The only antecedent in this passage is 'very few people'. So, grammatically, the pronoun 'they' can only correctly refer to 'very few people'.
By using the words 'directly', and 'although', and the phrase 'without realizing it' the writer has explicitly stated that 'they' and 'very few people' are separate and distinct groups.
Therefore, to answer the question: "What does the 'they' stand for here?"
'They' refers to some or all of the persons who are not identified by 'very few people'.
Brian Litton 2012
This is in complete agreement with my original answer.
I would rewrite the original passage as follows:
In the early days, very few people interacted directly with database systems. Others, without realizing it, interacted with databases indirectly through printed reports such as credit card statements, or through representatives such as bank tellers and travel agents.
Of course there are several possible ways to rewrite the passage while retaining the original meaning and avoid the ambiguity of the original pronoun/antecedent disagreement.