I think they categorize the stations as active rock and mainstream rock stations (see below) etc., so they get different charts.

Active rock is a radio format used by many commercial radio stations across Canada and the United States. Active rock plays current rock artists with a mix of classic rock songs.

Format background
An active rock station may include songs by known and popular artists such as Aerosmith, Led Zeppelin, Metallica, and AC/DC in its playlist, whereas a modern rock station would not. Conversely, unlike classic rock stations, an active rock station also plays music by popular current and new rock artists.

Similar to active rock stations, mainstream rock stations play current rock music, but concentrate more on classic rock than active rock stations do.

A pioneering station of this format in the late 1980s was WIYY "98Rock" in Baltimore, Maryland. Other early adopters of this format by the beginning of the 1990s include stations KISS "99.5 KISS Rocks" in San Antonio, TX, WAAF in Boston, Massachusetts, WXTB "98Rock" in Tampa, Florida and KEGL, "97.1 The Eagle ", in Dallas/Fort Worth, Texas. Satellite radio channels include XM's Squizz and Sirius's Octane.

Active Rock Airplay chart
Active Rock Airplay Chart is a chart that compiles the current hits on Active Rock radio stations and is used as a component for the Billboard Mainstream Rock chart. This chart is exclusive to R&R, with forty positions on this chart and it is solely based on radio airplay. 62 Active Rock radio stations are electronically monitored 24 hours a day, seven days a week by Nielsen Broadcast Data Systems. Songs are ranked by a calculation of the total number of spins per week with its "audience impression", which is based upon exact times of airplay and each station's Arbitron listener data.

Songs receiving the greatest growth will receive a "bullet", although there are tracks that will also get bullets if the loss in detections doesn't exceed the percentage of downtime from a monitored station. "Airpower" awards are issued to songs that appear on the top 20 of both the airplay and audience chart for the first time, while the "greatest gainer" award is given to song with the largest increase in detections. A song with six or more spins in its first week is awarded an "airplay add". If a song is tied for the most spins in the same week, the one with the biggest increase that previous week will rank higher, but if both songs show the same amount of spins regardless of detection the song that is being played at more stations is ranked higher. Songs that fall below the top 20 and have been on the chart after 26 weeks are removed and go to recurrent status.

http://en.wikipedia.org/wiki/Active_rock

Mainstream rock (sometimes called Heritage Rock) is a radio format used by many commercial radio stations in the United States and Canada.

Format background
Mainstream rock stations are between classic rock and active rock on the programming spectrum, in that they play more classic rock than active rock stations, but play more modern rock than classic rock stations. In many ways, mainstream rock is a successor to the widespread album-oriented rock (AOR) format created in the 1970s.

As of 2008[update], examples of mainstream rock stations in terrestrial radio include WLUP in Chicago, IL, KRXQ 98 Rock in Sacramento, CA WEBN in Cincinnati, OH, WAPL in Appleton, WI, KZRR in Albuquerque, NM, KEZO in Omaha, NE, WDVE in Pittsburgh PA, WHJY in Providence, RI, KSQY in Rapid City, SD, WAQY in Springfield, MA, KSHE in St. Louis, and KZOZ in San Luis Obispo, CA. Most have a very long heritage that dates back to the 1970s as AOR stations, which is why several trades like Billboard and R&R will refer these stations as "Heritage Rock.".

Rock Airplay chart
Rock Airplay Chart is a chart that compiles the current hits on Rock radio stations and is reflected as a component in Billboard's Mainstream Rock Tracks chart. The Rock Airplay chart is exclusive to R&R, with thirty positions on this chart and it is solely based on radio airplay. 24 Rock radio stations are electronically monitored 24 hours a day, seven days a week by Nielsen Broadcast Data Systems. Songs are ranked by a calculation of the total number of spins per week with its "audience impression", which is based upon exact times of airplay and each station's Arbitron listener data.

Songs receiving the greatest growth will receive a "bullet", although there are tracks that will also get bullets if the loss in detections doesn't exceed the percentage of downtime from a monitored station. "Airpower" awards are issued to songs that appear on the top 20 of both the airplay and audience chart for the first time, while the "greatest gainer" award is given to song with the largest increase in detections. A song with six or more spins in its first week is awarded an "airplay add". If a song is tied for the most spins in the same week, the one with the biggest increase that previous week will rank higher, but if both songs show the same amount of spins regardless of detection the song that is being played at more stations is ranked higher. Songs that fall below the top 20 and have been on the chart after 26 weeks are removed and go to recurrent status.

http://en.wikipedia.org/wiki/Mainstream_rock