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They were worried about the militia either being disarmed or made impotent by a strong federal government with either a national militia, or control over the state militias, or a standing army. The clear intent of the second amendment, as evidenced by its preamble referring to the militia, and by the discussion and debates that occurred at the time, shows that it was clearly intended not to refer to a personal right, but rather in a military sense.

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As has been pointed out by others, they may indeed have been "worried" about this possibility (and I think you are probably right that it was foremost in their minds), but that doesn't mean that "the people" = "militia members only". They might have been worried about any number of things, and the preamble could have been about anything at all ("George Washington having false teeth, the right of the people to keep and bear arms shall not be infringed.") -- but it is still the right of the people that is being reaffirmed, not the right of any collective organization. The preamble is more of an assumption or justification -- i.e. we assume that this right is going to strengthen non-federal militias, and is necessary for the security of a free state, therefore...