Well, apparently they were. There was, as far as I know, no restriction on not having any other connector on the device with the 'dock connector'. Given it seems Apple have seen some degree of sense, it's probably fair to say the licensing terms are
now roughly equivalent to the preceding ones.
As it is, as long as Apple provide relevant adapters to standard connectors (i.e. microUSB) it's unlikely the case for 'anti-competition' will be strong enough to run. With a way to plug an iPhone 5(etc) into non-lightning peripheral and now no restriction on how non-Apple connectors are supplied, I think that boat may have sailed. If Apple had continued with their 'us and no-one else' policy there might have been enough leverage to pursue a case but if that clause has been dropped, I think the case goes with it.
The lightning connector of itself is not anti-competitive, because peripheral makers can happily ignore it. It's technically in breach of the EU standard connector ruling but since that was watered down with an 'or an adapter' clause, that's effectively no ruling at all.
Indeed but it's not in their interests for it to be 'free' either. They want the accessory ecosystem to remain - it's their one remaining trump card over the opposition - but they want a piece of the money that's being made by it.
I'm not sure Lightning connectors will ever be as cheap to manufacture as dock connectors are/were. It's a more complicated interface although the actual plug is simpler. Plus I don't think the new generation of Apple products will ever dominate the market the way the older generations did. Many accessory systems are moving to wireless connections (bluetooth or wifi/'airplay' style) and thus can be multi-platform and don't need a lightning connector or port anyway. Eventually the only add ons that do have a cable still will be those that are used for charging. And even that may be on the way out - I reckon it's only a generation or two before wireless or at least 'surface contact' charging is common.