There are some obvious reasons to not be able to check in online, like a lap child where they have to verify age.
However, for an ordinary adult traveler - they most likely have a 4-S (SSSS or Secondary Security Screening Selection) boarding pass. I'd allow an extra hour for security screening, if you're traveling through a smaller airport. Major airports get enough 4-S screenings that it's not such a production, but last time my husband was 4-S'd at our local airport it took them 35 minutes to get the person who could do the screening to our security gate. The actual screening is not a big deal though - you go through the puffer, they hand search your bags, explosives wipe-down, sometimes a pat-down or hand wand.
In theory, selection for SSSS is mostly random. In practice - I've never been selected, and my husband is selected
every time he flies, unless the ticket is on his employer's credit card. He's been pulled for special screening since before the TSA existed though (yes - we know why, no - it can't be fixed, yes - I'd encourage him to do it again) and we're pretty familiar with the drill.
The best ways we've found to make it a quick and painless process:
1) That person should -have- a carry-on. Put everything except your photo ID and your boarding pass in the carry-on -before- you approach the security checkpoint. That way there's only one bag to search, one bag to keep track of, etc.
2) If someone in the security line makes a fuss about unannounced changes in policies and procedures, explain (in a moderately loud voice) why such things increase security (regardless of your personal convictions, even if the most positive thing you can say is "Front line TSA employees don't set policy, so making their lives more difficult won't get policy changed."
3) If you're traveling with small children - a toy in the top of the carry-on seems to diffuse tension. Fiction books, particularly paperback mainstream best-sellers with a bookmark in them are a good second choice.
4)Pass the metal detector on the first try. Make sure there are no coins in your pocket. No metal on your belt if you can help it. Check and double check -before- you approach security.
5) The rest of the traveling party should clear security and move past the benches to wait. It should be fairly easy to identify the "bright line" that TSA supervisors want you on the other side of (10 ft or so past the benches usually works). Even better would be to agree to meet at a further location (coffee kiosk, bookstore, gate, etc) so that you aren't lingering if that person is delayed.
6) Don't pass things back and forth between the SSSS individual and the rest of the party. Once you are in sight of security - what's yours is yours and what's theirs is theirs. As much as is reasonable, we try to follow that from the moment we enter the airport.
This is all pretty basic social engineering, but it means that once we get a TSA agent who can do the SSSS screening, it takes very little more time than a normal screening, and frequently less. If you're inclined to kick up a fuss and protest the violation of your rights/terrible effects of the TSA on humanity/worthlessness of such screenings - I'd
budget more like an hour and a half to pass the security checkpoint.
Oh, and if you're going to do something allowed but not standard (medical liquids/devices, or milk for a toddler for example) - don't involve the SSSS person unless you absolutely have to. It will just slow things down.