It's mostly a cost thing, the U2 flew very very high, the wiki puts it at 70,000 feet, very few planes can even fly that high, so planes can't really do an intercept, also it's altitude is above the design range of most radars. Radar searching for planes puts most of it's power in areas where they will find planes, so they are pointed to not look too much into the 70k ft flight area, they could probably pick it up, but it probably wouldn't track it through the whole coarse over the coverage area. The same radar could just be pointed up and it would do a much better job at tracking it, but that would significantly reduce the range of the radar. The only real option to take it out is then a SAM that can hit things at 70k ft, when the U2 came out, things just didn't fly that high, SAMs simply couldn't fly that high either, now with modern planes many will hit it, but ultimatly it is a cost tradeoff, like a space ship adding a little bit of range means more fuel, and you need more fuel to carry that extra fuel, it all adds up, twice the distance on the missile means much more than twice the size (and cost) without increasing any speed/damage/maneuverability specs. Once the missiles came out that could hit those altitudes they came out with an SR-71, basically even if you did see it, your missile would need a range of something like 100 miles at mach 5 to get an intercept coarse, that in a huge amount of fuel when you consider even today, things like a sidewinder only goes 22mi at mach 2.5.