They will charge the maximum the market is prepared to pay - that's capitalism.
Not exactly... the right way to look at this is they SHOULD charge a price that will bring them the most over all PROFITS.
Sure you might be able to have a cover price of $29.99 and 'some' may pay it... Sell it for $1.99 and (hopefully/potentially) a whole lot MORE will pay it. The 'perfect price' is a hard thing to come up with, it actually takes a far amount of research and testing.
A 'Molecular Biology Monthly' with a $19.99 cover price might sell 10,000 copies however dropping the price to 3.99 may NOT increase sales all that much given the specific audience the magazine caters to. Where a 'Fashion Monthly' with a cover price change from $19.99 to $3.99 will almost assuredly see greater sales (much greater) and even if the 'total sales' turns out to be the same bottom line profit when you compare 19.99*sales vs 3.99*greatersales, it's STILL a bonus since the larger reader base translates into higher AD rates and higher profits. It can even be argued that even if 19.99*sales vs. 3.99*greatersales is LESS of a profit on 'magazine sales' the greater AD revenue more than makes up for it.
Finally that only goes so far... for example a magazine that is given away 'free' doesn't automatically warrant EVEN GREATER AD rates... Since the advertisers wont value the readers as great as they would if the people had to actually pay for the magazine. People paying for it are far more likely to want read it and/or spend more time reading it.