"Thank you for your patience" is the routine way to make it polite.
Yes, the same words in a different form could be considered presumptuous. Like I just had some charity call me and basically say, "thank you for donating" when I had not yet agreed to anything. I considered that presumptuous. But "Thank you for your patience" is a routine, polite form of "please be patient". It is considered to sound less demanding.
You could try to invent your own polite phrase. But there is much to be said for using the conventional phrasing. When you use the conventional phrase, people read it and accept it without thinking about it very much. If you invent your own phrase, they're more likely to say, "Hey, exactly what does he mean by that?" That is, whoever the first person was to say "thank you for your patience", maybe the people he said it to thought, "that's rather presumptuous, what makes him think I'm willing to be patient?" But now that it's been used a million times, few people think that. If you were to come up with some new phrase, people might actually think about what you said and what the literal words mean.