(1) Protestants could not speak openly against the Queen (Bloody Mary Tudor) without retribution so they spoke in more or less a code to wit:
Mary Mary quite contrary
(Mary is a disagreeable Catholic tyrant)
How does your garden grow?
(the garden referred to is filled with the graves of protestant martyrs/opponents of the Queen and the growing number of such victims under her oppressive rule)
With silver bells and cockle shells
(instruments of torture such as thumbscrews and iron masks)
and pretty maids all in a row
(instruments like the guillotine known as maids to behead enemies)
they were Catholic nuns; or Mary's miscarriages.
or if the rhyme really is about Mary Queen of Scots, the maids are her ladies in waiting.
More on the lore of nursery rhymes here.
And here's the quilt being put together:
Pretty maids, it turns out, is a nickname for meadow saxifrage, a small white flower with four petals (Saxifraga granulata).