Here's something the publisher of June, a yaoi 
magazine said about it:  

Question: Why are female readers so attracted to 
love stories about gat makes?

Sagawa: The stories are about males, but the 
characters are really an imagined ideal that 
combine assumed or desired attributes of both 
males and females. Thus the heroes can be 
beautiful and gentle, like females, but without 
the jealousy and other negative qualities that 
women sometimes associate with themselves. . . . 
Also girls and young women in Japan still have 
constraints on them socially. They feel that the 
characters are freer if they are males, both 
socially and sexually. 

(Dreamland Japan by Frederik L. Schodt) 

To sum it up, the male character being chained up 
in the cel isn't really a male, but a safe female 
substitute. It's one reason the sex roles in yaoi 
are so defined -- one's macho, and the other 
takes on the role of the female. 

If there was a man holding a woman in chains, of 
course women wouldn't feel comfortable about the 
image; but when you have two men, there's the 
natural assumption that they're both on equal 
groups with respects to power, socially and 
politically. Take women out of the equation, and 
you can take a sado-machoistic theme in romance --
 suffering for the one you love or being made to 
suffer by them -- to the extreme with a safe 
female substitute. 

(As a side note, knights during the age of 
chivalry would take the role of the sufferer. 
There was a German knight, who sacrificed his 
little finger and countless injuries in duels, 
where he was dressed up as Venus -- I'm not 
making this up -- for a woman who insulted and 
abused him at every turn. The more she spat at 
him, the more devoted he was.)