Through the ages of mutual life, relations between Wizards and Muggles were not so simple, as some Wizards historians try to present to their readers. Even the greatest Wizard historian of XX century, Bathilda Bagshot, in her brilliant "History of Magic" described a lot of persecutions, tensions, tortures and even killings from both sides - but strangely never mentioned about good relations or co-operation between Wizards and Muggles.
Though we have a lot of historic evidences, that relations depended not only on "barbarism of Muggles" but from Wizard’s attitude and behavior. Those Wizards, who were "Muggle-lovers" (as they named by "pure-Wizard" adherents), despite of all risks, try to help, cure and support their Muggle-neighbors and get back love, respect and esteems.
Let`s remember that some prominent Wizards worshipped by Muggles as Saints - Muggles use this word not only like Wizards, to describe somebody, who bring us Spirit of Source of Sorcery, but also for those human beings, who did something outstanding for the benefit or were victims for their good deeds.
For example, we can count among them Adalgott, who invented shining sheep bell, to protect Muggles` livestocks from the wolves and who protected his neighbors from werewolf Canine the Black; Vodoaldus, who stopped the plague near the Soisson at 8th century, or Balderich, who was Muggle-born and did a lot for establishing good relations between Wizards and Muggles.
Personally I loved story of Golindukha the Persian. She lived at 6th century in Mideast. She was a Muggle-born, found by Al-Mansour when she was 19. Under his teaching she became a most powerful Witch of her times. But she has never used her power against Muggles, despite of all their tryouts to torture and kill her. Imprisoned and tortured, she stayed peaceful and lenient. Muggles threw her into the deep hole in the ground together with a big snake.
But Golindukha were a Parselmouth and sent it to find food for them both. Also she is considered as an inventor of Invisibility Cloak and used it to avoid Muggles` attacks. Muggles understood her deeds as a Miracle and still worship Golindukha till nowadays.
Golidukha understood that sources of Muggles fears are not barbarism, but uncertainty and weakness, and never blamed them.
Another story described us the life of Gregory Thaumaturgus (app. 213-270 AD),
who lived and died among Muggles and used his magic a lot for curing and supporting them.
During the persecution ordered by Emperor Decius in 250 AD, Gregory himself fled into the surrounding mountains with many from his Christian Muggles flock. His enemies pursued Gregory and his deacon to one of their hidden places, but when they arrived, he had transfigured the Christians into the trees and repaired them after enemies got out. When the persecution ceased, Gregory had returned to his city Neocaesarea, and cured many of his flock from the plague.
But we should not think that we can find such stories only at ancient times. One of the modern Wizards, John (Maximovitch) the Wonderworker, (1896–1966), was a prominent Eastern Orthodox ascetic and hierarch of the Russian Orthodox Church. He fulfilled a lot of miracles to protect his Muggles flock, but, due to the International Statute of Wizarding Secrecy he worked silently and humble. Right before his death, he put Incolumis Charm on his body to keep faith in Muggles further.
Great Albus Dumbledore wrote in his Notes to Tales of Beedle the Bard: "Beedle was somewhat out of walking in step with his times by preaching a message of brotherly love for Muggles." And Dumbledore on his own, who has gone through some misconceptions in his youth, became a biggest Muggle-lover and greatest wizard of modern times altogether.
I mean, that wizards should understand - not only secrecy and hidden life could keep safety and prosperity of W-community. But respectful, helpful and co-operation attitude of Wizards will do the job.