There are a few factors:
Supplements don't get absorbed as well as food sources
Vitamin B12 from supplements is absorbed at a rate ~50% lower than food sources
Formulation must be able to cover more cases than just vegetarians / vegans
Marketing claims such as "one per day" need to be upheld by the formulation of your supplement. Considering that supplements have lower absorption, there are several medical conditions (e.g. celiac disease and gastric bypass) AND medications (e.g. omeprazole, cimetidine and metformin) that interfere with absorption of vitamin B12, the formulation needs to account for those too in order to uphold the claim.
Furthermore, in some cases like celiac, the recommended dose is 1000mcg and there is no drawback on someone who doesn't need that much to consume this dosage, so they just make it like this.
The RDA (rounding up) is 3mcg. Considering the first factor, a supplement should contain 6mcg. That's 0.006mg. Or 0.000006g. That's a SUPER low dosage, which is very difficult to handle in industrial settings - you are going to need large amounts of excipient to pad up volume to form the pills in the right dosage and even then it is going to be difficult, requiring very specialized equipment. Furthermore, those pills need to be checked to ensure that they deliver the same dosage of B12 for every pill, and the lower the concentration, the more difficult it is to test it accurately - again, requiring specialized equipment and methods.
Since there are no ill effects of a larger dose and also considering the second factor above, is more viable and cost effective to produce a 1000mcg supplement
Source: NIH for the first 2 factors and yours truly, an industrial pharmacist, for the third