For someone totally new, just sampling to see which if any flavors they like, getting a bunch of 3ml samplers simply works for them. They can try 5 flavors for just slightly more than the cost of one 30ml.
The pricing scheme is consistent with other flavor vendors, whether they are just passing through the cost directly with a small markup or simply following the model used for flavor sellers. Look at Natures Flavors, 1 ounce of something is $12.50, while 16 ounces is $49 -- it's a factor of 4 cheaper to buy by the pint. For a steeper example, try perfumers apprentice, 4ml of Bavarian Cream is $1.40, while 30ml is $5.50; it might seem silly to buy just 4ml, unless you are unfamiliar with the products and want to test multiple.
At a reseller level, if a person does a rebottle, breaks say a 16 ounce of flavoring into smaller ones, the cost of the flavoring is relatively small, it's the cost of the resale bottles and touch time to make the labels, etc. A 3ml bottle runs 40 cents, while a 30 ml is $1. 3 ml of the flavoring may have cost 50 cents, while 30 ml is $5. That gets you to about $0.90 and $6.00 base cost. The seller may be choosing to only charge $0.60 for the time to label the little one, with $1.00 to label and obtain markup on the bigger one.
(Extra Credit: come up with the rationale on TPA's tobacco blend alc pricing. 15ml at $3.80, 30ml at $10

I always buy multiple 15ml, Linda has had consistent pricing on it all year. The tobacco blend PG pricing actually makes more sense to me, but I buy the alc version since I DIY some 0PG, easier to stay with just one flavoring rather than buy both variants. I actually just sent TPA an email to see if it is a whoops in pricing.)