During the 6 seasons of the past 9 (not counting this year) that Iowa State beat Iowa, their record was 37-35, whereas Iowa's was 32-39. Your suggestion that every time Iowa State beats Iowa, they finish the season 1-11 or 3-9 and happily proclaim the season a success "because we beat Iowa" in no way reflects the reality of the situation. I will break down each season's record for you:
1998, Iowa State 27, Iowa 9 (Iowa State: 3-8, Iowa: 3-8 -- Yes, this was close to the "3-9" record you presume, but Iowa was not a good team that year, either. One can hardly say that Iowa was the superior team that year and should have won.)
1999, Iowa State 17, Iowa 10 (Iowa State: 4-7, Iowa: 1-10 -- Iowa State's record was a bit deceptive that year. They lost 4 games by a total of 17 points, including heart-breaking losses to nationally-ranked Kansas State and Texas. These games exposed a disturbing trend of Dan McCarney-coached teams being unable to finish strong in tight games, but Iowa State was actually a more competitive team in 1999 than the record reflects. The 1999 Cyclones were clearly better than Iowa -- which was mired in in one of its worst seasons ever.)
2000, Iowa State 24, Iowa 14 (Iowa State: 9-3, Iowa: 3-9 -- Iowa State won their bowl game and finished the season in the Top 25. There's no disputing which team was better this year.)
2001, Iowa State 17, Iowa 14 (Iowa State: 7-5, Iowa: 7-5 -- The Cylcones won a close game between two evenly-matched teams.)
2002, Iowa State 36, Iowa 31 (Iowa State: 7-7, Iowa: 11-2 -- No question, Iowa was the better team at the end of the season, but the Cyclones' victory was by no means an upset at the time of the game. After beating Iowa, the Clones ran out to a 6-1 start and were ranked 9th in the country. Then the wheels came off, and Iowa State closed out the season at 1-6 with a bowl loss to Boise State. Every Iowa State fan I know considers this season a major disappointment, even with the win over Iowa. Still, 7-7 and participation in a bowl game is a far cry from 1-11 or 3-9.)
2005, Iowa State 23, Iowa 3 (Iowa State: 7-5, Iowa: 7-5 -- Based on expectations to start the season, Iowa fans were bitterly disappointed with the outcome of this game. But once again, this game was no upset, despite Iowa's 8th-place ranking in the national polls. By the season's end, it was pretty clear that the two teams were comparable in terms of talent and competitive ability.)
Where are all those 1-11 or 3-9 Cyclone teams you are referring to? This has been a very evenly-matched rivalry over the last 10 years. If Iowa fans are honest with themselves, they have to admit that Kirk Ferentz's run of great seasons from 2002-2004 cannot be said to accurately reflect the current state of the program. I'm not saying he can't ever get them back to that level, but they're not there now. Based on where the Iowa program is right now, no one can confidently assume that the Hawks could win 24 of their next 32 games. To expect Iowa State to accomplish that when it's not a given that the Hawks can do it themselves is nothing short of a double standard.