There's actually good reasons to use both polyester and cotton for potholders and the like, and you choice is probably going to come down to personal preference.
Polyester is considered flame-retardant, and wont catch fire till 824 degrees Fahrenheit (440 C) The problem is that polyester melts at only 428 F (220 C) and melted plastic will stick to clothes and skin which can cause severe burns.
Cotton will catch fire at 410 degrees F (210 C), maybe more depending on how tightly packed it is, but the danger is mostly just the fire itself rather than the material it leaves behind.
There's really only one bad choice and that's using both. Cotton-poly blends melt AND burn. It's the worst of both worlds.If your fabric is cotton, use cotton thread. If you want to make really safe, fire-resistant pot holders, buy some of that synthetic fabric with the fire-retardant already in it, and use poly thread.