He is the originator of the modern novel; indeed, you could say that he is the originator of modern narrative — that the war reporter and the thriller writer owe as much to him as the avant-garde fictionist. The great bear of Croisset, the monkish aesthete who spent much of his life in one house, and a great deal of that time in one room, has sired thousands of successors.
Much of the time Flaubert's influence is too familiar to be visible. We so expect it that we hardly remark of good prose that it favors the telling and brilliant detail; that it privileges a high degree of visual noticing; that it maintains an unsentimental composure and knows how to withdraw, like a good valet, from superfluous commentary; that it judges good and bad neutrally; that it seeks out the truth, even at the cost of repelling us; and that the author's fingerprints on all this are, paradoxically, traceable but not visible. You can find some of this in Defoe or Austen or Balzac, but not all of it until Flaubert. And after Flaubert, it sometimes seems, this is all you can find.
I was unimpressed with Flaubert because the subject matter didn't do much for me, and the style didn't seem special. But it is clear that the reason the style didn't seem special is because Flaubert influenced all future writers of prose. It's not that he's not special--it's that he was the first to write like this, the first to be special, and was so influential that his style is now difficult to distinguish from the style of many novels written since Bovary.
We don't always appreciate the real innovations, because if they are innovations with impact, they begin to seem a lot like everything else. But we need to know enough literary history to recognize who was the first.
I feel the same way about the multiple endings of John Fowles' The French Lieutenant's Woman. Today the endings can seem gimmicky. Belonging to a generation in which everyone has seen Wayne's World, the idea of giving multiple endings to a narrative might not seem that special. But I cannot think of anybody who had done this before Fowles (if you can thing of somebody, let me know). Fowles seems to have created something entirely new with this concept.
When evaluating and interpreting a work of literature, the bulk of your interpretation should come strictly from the text. But historical context is worth something. It is only with some knowledge of historical context that we can begin to appreciate the innovators of art.