I think in terms of numbers F1 would draw more attention. Bike fans here are numerous but in terms of popularity it has toppled. In the best years eg. 1999, when Crivillé and Alzamora were 500cc and 125cc champs respectively TV audience toppled at around 4 to 5 million, and that's as good as it gets, F1 last year reached 7 or 8 million at times, something only football (soccer) can achieve in this country.
The difference I think is the loyalty of the fans, even in the bad times bike fans still watch the races and attend the races, while in F1 if Alonso crashes out, people just change channel. F1 is quite new to most Spaniards cause there was nothing remarkable before Alonso, so I guess although it's very popular, it's not stablished.
Although I guess Alonso may change this situation if he keeps beating the crap out of Schumi and Co.
There's also a political issue, most Spanish riders are Catalan (Sete, Pedrosa, Checa, Elías ...), there's a confrontation now in Spain between the Catalans and the rest of Spain and it affects everything including sport. For example many more people followed Fonsi Nieto (from Madrid) in his fight for the 250cc title in 2003 than next year's sweep by Pedrosa.