As someone who tracks people and their habits for a living, I will share a few observations about the average user.

Implications of the phone information collection initiative on the internet:

There will be a little more activity online worrying about privacy. The twitterverse will "explode" momentarily, but people will be aware of this as something going on in American government for about a week until it falls out of the mainstream media (where most people get their "news"). Then they'll stop talking about it. Most people who feel they are doing nothing wrong will feel they have nothing to worry about (most people are feeling people). Paranoid people will try to figure out how to hide things and [unknowingly] make themselves look more like people of interest. These are the people who think the government is always watching them, when in actuality the government is looking for patterns of usage that don't stick to the norm (so these people likely do pique interest, but they aren't ever really monitored because outside of a few similarities they will continue to act normally for themselves).

Successful, "Bad" people are much better at blending in with society than these people.

Will it gain anything for the government? Not really other than allowing them to be able to connect a few dots for communications in the past. (The information will be overwhelming.) Politically it will be more damaging (which is what I, myself think this is all about anyhow). If people were doing bad things on throw-away phones chances are (if those people are moderately smart) the phone with the bad-linked IMEI identifiers have been discarded, sold, or donated. It just makes the ignorantly "bad" people realize that they have to be better about their habits.

Knowing this, what steps can ordinary individuals take to safeguard themselves against the collection, and exposure, of such sensitive personal information?

Unfortunately statics are not on their side. Most "ordinary individuals" or average people don't have an intellect where they can begin to fathom what is possible with such numbers (identifiers). When they try to research it they can become really good at this one thing (if they have the luxury of focus), but they likely fail elsewhere and most of them are too busy to even worry about it because they have real-world problems going on. To the average American it will be one more thing that focuses on something other than what they feel they need. They'll likely see this as money being spent on something other than the necessities, which for them are going to be things like education, food, and public aid... things that above average (non-ordinary) people take for granted. Things that poor people fear losing because it is unfortunately out of their control.

Ordinary people might notice that there are fewer phone cards on the racks at big box retailers because of the spread of paranoia and because that's where they buy things.

Similar to what Rory Alsop was saying, most people will likely not be able to tell you the difference between their monitor and their computer (if they use a desktop) and they often think of electronic mobile devices as some little bit of magic or mysticism that works in some form or fashion they care not to know about. Or they consider them luxuries, gadgets, or toys. As long as it works, they are not concerned with the technology.

Overall security will increase, knowledgeable people will raise the bar; as always.

If you're in the know, then you likely know that there is nothing that you can do to stop this sort of thing from happening and go about living a normal "good" life. If you want to try and obfuscate all of your communications, or live off of the grid, you may feel more comfortable in mind, but I can tell you this is much harder. People are tracked everywhere they go.

Simple example:

Typical user buys a phone card at a big box retailer. They user their debit card (or some other traceable card). They go home and turn on their computer. They connect to the internet with a non-encrypted connection. They go onto Facebook, Twitter, Yahoo, or countless other sites where they receive numerous tracking cookies. Then they go onto the website where they re-up their phone by punching in the numbers from the card they purchased, or enter the numbers on the phone itself to add more minutes. They may use this phone to connect to their social media profile directly where they have downloaded a tracking app. The phones all have built-in tracking under the guise of "user protection." This phone number is in their public profiles on social media and provided on every marketing survey, job application, and form they complete. They are traceable and fairly consistent (until they lose a job or something of that nature). If they lose their phone (with their "life" on it), they will keep the same phone number.

How can you not be this person?

Use cash for all technology related purchases. Do not register your purchase. Wipe whatever OS is on the device and use an open-source OS as the host platform. Or use an OS like Knoppix if you would like not to leave any traces. If you must run something like Windows, then run it under a VM. Activate but do not register it. Prevent all communications with companies that track you. You can do this with firewall rules on a hardware firewall. You can try to use something like TOR, but remember if they are monitoring your location, they are monitoring the location you are trying to reach because they have already figured out your pattern. Stop using credit cards. Stop providing your information freely on the web. (Domain registrations, Social Media, etc) Stop linking your habits to your person online. Be unpredictable. Wipe things that need to be erased. No keeping cracked copies of anything on anything that can't be destroyed with a blow-torch or a lighter. Think thumbdrives vs hard drives and SSDs.

Or better yet... unplug more often and stop worrying about it. Life is too short for this stuff.