The Cyprus flag is quite common the "Greek" side. You can see it hoisted in many places. It is more frequently viewed than the Greek flag. The "Greek" Cypriots are quite proud of their flag. Dov Gutterman, 28 May 1999
And yet it was deliberately designed to be a "neutral" flag, in order to inspire the peace between the two communities (Greek and Turkish Cypriots). The very same occurred with the Irish flag, where green stands for the Irish, the orange for the Protestants and the white for peace among them — the very same flag that was even prohibited in Northern Ireland because it may offend one of the conflicting parts! Other examples to hand are the unofficial green-white-pink flag of Newfoundland (similar symbolism as Ireland) and the Tatarian flag with green for Muslims/Tatars, red for Russians and white (very thin stripe!) for peace. António Martins, 29 May 1999
The [previous] flag of Bosnia and Herzegovina was already a compromise design; this specifically-designed neutral flag [has] received a political charging which now makes it unacceptable. John Hall, 18 December 1997
Other cases are:
USA Grand Union Flag 1775-1777: This flag altered the British Red Ensign with six white pieces of cloth to create a field of 13 red/white stripes. By 1777, the presence of the Union Flag in the canton was deemed inappropriate.
Cambodia: The flag of UN blue with a white map and blue text ofthe name of the country was an interim flag that wasn't appreciated much at the time (early 1990s), but now is used by Cambodian Americans. Probable the reverse of the original question [compromise flags that became politically charged and unacceptable].
The 1928-1994 flag of South Africa was really a compromise between the British and the Dutch. They conveniently forgot the majority population which is now quite well representated in the government and in the flag. Nick Artimonich, 18 December 1997
This is, although interesting as a compilation, a bit too inclusive what regards flags of pacifism: Olympic flag, Suffragette flag, Christian flag, gay pride flag and all.
Over and over again there is this reference to the white flag in the writings of Tacitus. I have neither found chapter and verse for a good reference nor have I found the "white flag" thing myself by searching the texts. Does anyone actually know where this really is?
Regarding the Rainbow "PEACE" flags, the chronology is wrong: Aldo Capitini in 1961 was not the first using the rainbow flag as a peace flag in Italy. This was already in use since at least the late 1940s in the context of the Communist Party (PCI), usually, but not always, with the inscription "PACE." M. Schmöger, 12 October 2015