Seeds from the seed maker are not free. The machine doesn't make them out of thin air. Yes, it outputs seeds, but to do so, you have to input a crop, which has its own value.
Putting a crop through the machine will produce, on average, approximately 2 seeds, so let's take a look at some of the big money crops from each season and crunch the numbers....
A cauliflower has a base value of 175g, and so the two seeds would effectively cost 87.5g each, slightly more expensive than buying them for 80g each
A melon has a base value of 250g, the two seeds would effectively cost 125g, quite a bit more than buying for 80g each
A pumpkin has base value of 320g, the two seeds would effectively cost 160g, again quite a bit more than buying for 100g each
Even at base quality, you can clearly see that all of these are actually a losing proposition, compared to just selling them raw and buying new seeds. Once you factor in the 10% price boost from the Tiller profession, and then on top of that add the quality bonuses for silver and gold, the losses just build up. For instance, a gold pumpkin is worth 528g, so the two seeds it makes cost 264g, more than 2.5x the cost of just buying a seeds.
And if you had the opportunity to process them in a keg or a jar, you're losing out on an even larger amount of money. Going back to the pumpkins, Pumpkin juice sells for a whopping 1008g with Artisan profession. If you stick it in a seed maker instead of a keg, those seeds have an effective cost of 504g.
Your theory only really works with the very cheapest crops, such as tulips, at base quality or sometimes silver quality. As the crops get more valuable, the losses mount up.
As a money maker, if you have a lot of seed makers, and a lot of blueberries or cranberries, it is also a reasonable option for quickly increasing the value of the crop. For instance, a 50g blueberry becomes 2 blueberry seeds worth 80g, in just 20 minutes.
The seed maker is, however, the only reasonable way to generate seeds to grow lots of ancient fruit, as the seeds cannot be purchased.