The concerns in the past have been mainly to do with lithography; eg, when the feature size of the silicon went below the wavelength of the light we were using, we had to make masks that utilized difference patterns. This is a mere manufacturing problem.
But now we're getting to fundamental limits. Even if we had the ability to place the atoms however we wanted them, there's an intrinsic limit. You can't make a transistor out of half an atom.
We already hit a wall with frequency; for the longest time, it looked like speeds would go up and up. It's not an apples to apples comparison, because the Pentium 4 had a long pipeline, but a 3.8ghz Prescott was released in 2005 - which is exactly the maximum turbo frequency of the 2011 Sandy Bridge 2600k I'm typing this now on. Ivy has it beaten by just 100mhz.
Now, that's not to say that computation will stop progressing. But it's not going to look like last year's CPU just smaller for much longer; some pretty fundamental changes are going to have to be made. Dynamically reconfiguring memristor circuits are what excites me, but it's just as likely to be something else instead.
As far as flash memory in particular goes, I'm no expert, but cell durability is falling substantially with each shrink (on average; Intel bucked the trend with their 25nm flash), and so the usable limit to feature size may come more quickly than with standard transistors.
But the industry has managed to push through walls that seemed just as intrinsic before, so I wouldn't bet my life savings on it.