Looks like several subspices of blastocystis are resistant to several drugs that are considered active against blastocystis
I do not have full article of this, but looks like
32% of Blastocystis in this study were resistent to furazolidone
40% of Blastocystis in this study resistent to metronidazole/flagyl
100% of Blastocystis in this study resistent to ciprofloxacin
So yes Flagyl is clearly not the way to go, and tripple therapy is likely needed, because as you can see also considerably resistance to furazolidone, but together with other effective drugs it looks like it give high cure rate